For generations there has endured a certain liberal narrative of European history which would have us believe that the establishment of the Christian commonwealth (Christendom) is an inherently oppressive concept that leads only to repression and killing in the name of religion. To establish this point, the bugbear of the age of the religious wars is trotted out, and it is put forward as a simple fact of history that Europeans once killed each other by droves over minutiae of religion. The French Wars of Religion and the St. Bartholomew's Day Massacre are touted as examples of Protestants and Catholics murdering each other over obscure points of theology. These frightening episodes are supposed to be what liberal democracy "saved" us from, and thus provide the justification for the strict separation of Church and State found in most modern constitutions.
If we were to give any ground to the Church's moral and social claims, so says the liberal narrative, we would risk returning to this barbaric period when Christians slaughtered each other over creeds.
It behooves the dedicated Catholic to examine these claims and see if they have any merit. Does the existence of the confessional, Christian state necessarily lead to bitter religious wars? If so, then the liberal narrative may be justified in asserting that a radical separation of Church from Government was necessary to prevent religious disputes from erupting into theologically driven violence. If not, then the liberal narrative needs to be drastically revised or done away with all together.
If we take a brief survey of all of the major conflicts during the period of the Protestant Revolt and the succeeding period sometimes known as the Counter Reformation or the Age of the Religious Wars, it will become evident to anyone with even a cursory knowledge of European history that these were not really religious conflicts in any sense but the broadest (sometime one side happened to be Catholic and the other Protestant).
In every case without exception, the prime causes for the "religious wars" are much more bound up with class and regional struggles, dynastic-political fighting (sometimes under the guise of religion), land grabs by rapacious barons looking to capitalize on the chaos following the Church's loss of power in many places, and sometimes just raw exercises of power by emerging nation-states. In no case at any time were two armies fighting and killing each other over strictly theological questions.
Philadelphia Archbishop Chaput noted the prevalence of this myth in a recent article for Witherspoon Institute. The Archbishop states: "Early modern states spent decades at war with each other, ostensibly over theological differences. But, in reality, churches and states used each other for their own very practical ends. States grabbed the chance to expand their power, and churchmen sought protection and state support." The painting of these conflicts as purely religious has been a bait-and-switch fostered on our culture by modernists promoting a triumphalist secular narrative of history.
Let's look at these wars one at a time and inquire into their real causes, hopefully demonstrating that much more beyond religion was in play here:
Peasant's War (1525): The German Peasant's War was the first real popular uprising of the Reformation era. Throughout 1525, thousands of German peasants, inspired by the tumults introduced into Germany by Luther, rose up against the feudal overlords in an orgy of violence and killing that left 100,000 dead. Though one cannot deny that Luther's revolt added to the intensity of the uprising, it did not cause it. Neither the motivation of the peasants nor the knights who put down the revolt were religious. The peasants were reacting against the burdens imposed on them by the feudal lords and sought to establish greater autonomy. The motivations were political and economic and had much to do with the peasants seeking to protect the gains they had made over the previous century by the weakening siegnural system. The peasants were goaded on by a landless class of disenfranchised knights who sought to win power and influence at the expense of the destruction of the greater nobility, and it quickly became a class war of the peasant-serf against the landed powers (the nobility, but also the monasteries). Luther himself vehemently denied there was anything religious about the uprising and stated it was due to mere envy; the warlords who mercilessly put the revolt down cared nothing for maintaining any sort of doctrinal orthodoxy but only retaining political power. It is not even possible to really discern "Catholic" and "Protestant" sides in this revolt. It was a class struggle, pure and simple.
French Wars of Religion: The French Wars of Religion, which lasted from 1562-1598, are usually brought forward as the quintessential example of a religious war sparked over theological disputes, as it pitted the kingdom's Catholic faction against the emerging Huguenot faction. This series of conflicts is a favorite of liberal apologists because of the St. Bartholomew's Day Massacre bugbear. Yet, as in the case of the Peasant's Revolt, this conflict was not generally about religion, but about a power vacuum left by the premature death of King Henry II in 1559. While there had been sporadic religious violence in France prior to 1559, the King's death led to the rise of different political factions intent on seizing power and utilizing the religious sentiments of the times to bolster their claims.
The French Wars of Religion were really a power struggle between the House of Guise, the House of Montmorency, and the House of Bourbon. The Catholic House of Guise and the Huguenot House of Bourbon each played up their religious affiliations in order to garner support, and there was also a strong class divide involved as well - the Huguenots tended to be upper middle class and involved in trade, while the lower classes and peasantry remained solidly Catholic.
The St. Bartholomew Massacre, always put forward as the prime example of what religious intolerance can lead to, was initially not motivated by religion at all. The Protestant Admiral Coligny and his followers were believed to be plotting against the royal family in retribution for a botched assassination attempt. King Charles IX and Catherine de Medici had been warned by several credible witnesses, Protestants and Catholics, that some sort of Huguenot uprising was planned; there was an army of 4,000 Huguenots camped outside of Paris. Given these facts, the King authorized the killing of Admiral Coligny and a few other accomplices as rebels. However, after the death of Coligny, the violence began to spread throughout the city of Paris and then the provinces, despite the king's commands that it end. In the aftermath of the violence, King Charles IX explained his rationale for calling for Coligny's death, solemnly declaring on August 28m 1572 that the punishment of the admiral and his accomplices was due not to their religion but to their conspiracy against the Court. It was a political act done to suppress the Coligny faction that was an irritation to the Court and was believed with very good reason to be plotting an uprising. Coligny and his faction had been at open war with the crown three times in the past decade, and there was no reason to believe it would not happen again.
In pointing out that the Massacre was not a strictly a religious affair, it could be pointed out that many Catholics were killed in the violence as well. In general, anyone in Paris who was wealthy or appeared to be wealthy was a target, and class envy and a desire to be free from debt were motives just as much as religion. A number of bourgeois Catholic Parisians had suffered the same fate as the Protestants; many financial debts were wiped clean with the death of creditors and moneylenders that night." It was a massacre of the haves by the have-nots, and as in the Peasant's War, the chance of plundering wealthy homes was a large incentive to violence. 
As if to underscore the skin-deep nature of the religious aspect of these wars, it is also worth noting that, in the end, the wars were ended when the chief Huguenot antagonist, Henry of Navarre, flippantly converted to Catholicism in order to obtain the crown, with the famous phrase, "Paris is worth a Mass." Such shrugging complaisance hardly suggests a war fought be religious zealots over theological principles. Certainly, religion was a factor; certainly, as in the case of the Peasant's War, mobs could be animated by calls to religious piety by demagogues. But it is manifestly incorrect to assert that these wars were primarily about religion. They were about class warfare, factionalism at court, and the attempt to fill a power vacuum left by the untimely deaths of both Henry II and Francis II.
Scottish Civil War: The Scottish Civil War refers to those tumults in Scotland between the 1542 defeat of the Scots to the English at the Battle of Solway Moss and the final defeat and imprisonment of Mary, Queen of Scots in 1569. During this period Scotland was transformed from a Catholic kingdom to a Protestant Calvinist society. As in England and Germany, it was not due to a popular uprising from the people, but to the top-down acts of a cadre of unscrupulous, land-hungry nobles who were given moral legitimacy by some radical preachers (George Wishart and John Knox). The establishment of the new Protestant communion ("The Kirk") was to be financed by lands plundered from the Catholic Church, and the Protestant nobles ("Lords of the Congregation") were to exercise considerable control in this. As in Germany, a land-grab was involved; as in England and France, the "Reformation" was carried out during a Regency - that of Mary Queen of Scots - and so there is another element of an unruly nobility attempting to increase their own power over and against that of the Crown.
In several cases, the actions of the Scotch Lords of the Congregation are attributable to the fact that some were in the pay of Elizabeth and had a vested interest in promoting Protestantism in Scotland on behalf of the English, for whom religion and political policy were one and the same. Archibald Campbell of Argyll and James Steward Earl of Moray, two principle Lords of the Congregation, actively received support from the English against their own Regent (Mary of Guise). The religious sentiment of some of the lords is extremely questionable; for example, Patrick Ruthven, 3rd Lord Ruthven, was one of the most dedicated Protestant lords, but he was also a known warlock. All in all, the religious reformation of the Lords of the Congregation appears more of a political and financial power grab at the expense of a weak ruler (Mary Queen of Scots) based on Machiavellian principles than any sort of godly reform. Knox may have been truly motivated by religious motives, but if he was, he allowed himself to be taken advantage of by the Lords of the Congregation who could care less about Knox or Calvinism so long as their power was not threatened.
Spanish-Dutch War: The brutal attempt of the Spaniards to pacify the Dutch throughout the sixteenth century, though it pitted Catholic Spain against Protestant Netherlands, was hardly a religious war. It began out of the dynastic policy of the Hapsburgs who wanted to retain control of the Low Countries that Charles V had ruled and soon became a nationalist conflict. Catholic Spaniards sometimes killed Catholic Dutch, who were often times more sympathetic to the plight of their own countrymen, even if Protestant, than to the foreign Spanish; the executions of two prominent Catholic nobles, the Counts of Egmont and Horne, in 1567 shows that the Spanish were not just out to get Protestants, but anyone who opposed Spanish rule. Here we have nationalism, dynastic policy, and Spanish imperialism all mixed together with a smattering of religion.
Anglo-Spanish War: The celebrated Anglo-Spanish War that culminated in the defeat of the Spanish Armada in 1588 was trumpeted as a religious war at the time (Philip's desire to get rid of the "heretic queen" and Elizabeth's skillful use of anti-Catholic propaganda to galvanize her nation against the Spanish threat), but it must be admitted that, as in the case of some of the other wars we have looked at, the religious language was used to rile up support for these conflicts among the people. The fact that this language was used does not mean religion was the primary motive. In the case of England and Spain, we could easily cite growing conflicts over who would control the shipping lanes from the New World to Europe, the English alliance with the Dutch with its corresponding economic incentives based on the wool industry, and the imperialist policies of Philip II.
English Civil War: Moving into the 17th century, we have the English Civil War between not Protestants and Catholics, but Anglicans and Puritans. While many Puritans in this conflict undoubtedly were motivated by a desire to establish a "godly order" in England, such as Cromwell, most historians cite the schism between the personal rule of the Stuarts and the growing power and independence of Parliament, inequalities in Charles' program of taxation (the "Ship Money" controversy), and Charles' general unpopularity with the Puritan nobility in and around London. In a broader context, we could also cite the growing restlessness and independence of a burgeoning capitalists merchant class against the more traditional mindset of the Stuarts, who did not accept the principles of laissez-faire capitalism.
Thirty Years War: The Thirty Years War (1618-1648) is the final engagement of the age of the religious wars and was the least religious of all the conflicts of the era. Although it initially pitted Catholic Austria against Protestant Bohemia, it later got so convoluted that nobody but the most naive could seriously presume this was a religious conflict. There was Catholic kingdoms against Catholic kingdoms, Catholics allying with Turks against other Catholics, Protestants allying with Catholics against Catholics allied with other Protestants, Protestants versus Protestants and numberless bands of mercenaries who freely went back and forth between both sides. Look at some of the dizzying alliances of this war:
- Protestant Bohemia allies with Muslim Turks against Catholic Holy Roman Empire
- Catholic Spain allies with Protestant Saxony against Protestant Bohemia
- Catholic France allies with Lutheran Sweden against Catholic Holy Roman Empire
- Catholic France subsidizes Lutheran Denmark against Catholic Holy Roman Empire
- Catholic France against Catholic Holy Roman Empire
- Protestant Denmark allies with Catholic Holy Roman Empire against Lutheran Sweden
- Catholic France against Catholic Spain
The issues in this war were the territorial integrity of the Holy Roman Empire, the expansionist muscle-flexing of the new dynasty in Sweden, and the traditional rivalry between the Holy Roman Empire and France. Only the first phase of the war, from 1618 to 1625, can be even remotely consider religious, and even that phase of the war was closely bound up with nascent Bohemian nationalism. This war was not religious in any meaningful sense.
If we look at all these conflicts, we see a common thread: They all involve conflicts of primarily Catholic countries against primarily Protestant countries, and for this reason, it is easy to unthinkingly call them "religious" conflicts. Of course, the fact that two countries happen to have different religions does not make a conflict a religious one, even if the religions are in antagonism. By that thinking, the Mexican-American War would be deemed a "religious war" because one side was primarily Protestant and the other primarily Catholic. No doubt the opposing religions of the two sides in these wars made things more tense and made it easier for rulers of those kingdoms to use the cloak of religion to energize their populations to support these wars. Religion was always there as a factor, but in no case was it the primary or motivating factor. Religious tensions may have been a spark that set something off, as in the Peasant's Revolt, where Luther's preaching provided the religious backdrop that energized the latent economic and social grievances of the peasants, but in each of these revolts religion was a secondary consideration among many other issues, not the primary issue.
Yet, if we recall the liberal narrative, it states not only that the wars of this period were religiously motivated, but that the participants were actively fighting about religion, as if the Catholics and Protestants engaged in these battles were primarily killing each other over credal statements. This narrative does not hold up, and consequently Catholics ought to reject this narrative that would have us believe that the confessional Christian state leads to war; it was not the presence of confessional Christian states,
But it cannot be denied that this particular period in history saw an increase in both the number and the scale of wars. If religion was not a primary factor, what did lead to these wars? If anything, it was not Christendom and the Christian confessional kingdom, but the breakdown of Christendom and its supplanting by nationalist nation-states that precipitated these wars. In each conflict, perhaps except the Peasants Revolt, we see rising nationalism as a primary factor; instead of different noble houses fighting each other in contained private wars, we have entire nation-states fighting other nation-states in expansive, public wars. Nationalism, with its "us versus them" mentality that attaches too much importance to language, has fostered more wars than Christianity ever did.
We could also cite growing class divisions as a result of emerging capitalism; the Peasants' War was particularly motivated by class aggression, the landless knights riling up the lower classes to attack the nobility in last-ditch attempts at grabbing more land and wealth. Much of the Protestant resistance in the Thirty Years War was motivated by a fear of having to return confiscated Church property that was stolen at the time of the Reformation.
There have always been wars, and so long as there is religion, men will go to war with their religion in mind, sometimes giving them solace as they face great peril, sometimes riling them up against an enemy nation. Sometimes kingdoms of different religions go to war against each other, as when Catholic France fought Protestant England during the Napoleonic Wars. Yet, when we look at the nature of these "wars of religion" in detail, we see that what really occurred between 1525 and 1648 had more to do with emerging capitalism, the growth of nation-states, and the consolidation of central governments than religious creeds. The liberal narrative of the nasty age of the religious wars simply doesn't hold up.
 Archbishop Charles Chaput, "Life in the 'Kingdom of Whatever'", http://www.thepublicdiscourse.com/2012/11/6902/ [accessed 6 Nov. 2012]
 Frieda, L. (2003) Catherine de Medici, Weidenfeld & Nicolson, ISBN 0-7538-2039-0, pp. 314-16