The Protestant Reformation began in 1517. Over the next century or so, Germany, France and the United Kingdom would all be involved in their own immensely destructive civil wars. In the cases of Germany and France (the 30 Years' War and the French Wars of Religion), these wars were explicitly fought between Protestants and Catholics. In the case of the UK (the English Civil Wars), we see essentially the same division: Protestant Puritans against Anglicans and Catholics. In the 21st century, lots of people have an easy time saying that everything is political, and no one goes to war for salvation or to kill heretics and apostates; there's always some underlying, foundational struggle for political power. We often hear this refrain vis-a-vis Islamic extremists in the Middle East. But in the case of the great European wars of the 16th and 17th centuries, is that view true? These were the largest conflicts Europe had ever seen, and the largest conflicts Europe would see until the World Wars of the 20th century. Is it a coincidence that they followed the Protestant Reformation — the most consequential religious division Europe had ever seen? I doubt it, but I'm not an expert. So, to what extent were these massive conflicts political struggles, and to what extent were they genuinely motivated by religious and theological differences?
My main source here is going to Peter Wilson's *Europe's Tragedy*, an incredible (and incredibly long) look over the entirety of war from its origins to the effects of the war and its Peace on Europe in the decades after it ended. For the parts related to him specifically, I'm also pulling from Brennan Pursell's *Winter King*. Because of my own biases, I'll be focusing on the Thirty Years War, which in any event is the Big Daddy of the European wars of religion.
There's an underlying assumption here that bears addressing that also answers the quesiton. The assumption is that often, these sorts of wars are "political struggle" in a way that puts into question whether the participants are "genuinely motivated by religious and theological difference". This is a problematic assumption even now—radical Islamists like ISIS do have political aims in addition to religious and theological aims, but these are not at cross-purposes. Controlling territory as a state allows them the means to enforce their orthodoxy on others. For the sincerely religious, there is often no meaningful gap between political and faith in a religious war; political victories are religious victories and vice versa.
The same is true for most leaders involved in the Thirty Years' War: political and religious interests combined in powerful ways. The first and most obvious combination of these interests can be found right at the start of the war. If you remove religion from the case of Frederick V, the so-called "Winter King", you will just see a noble jockeying to win the Holy Roman Empire through the Bohemian Crown, and a Habsburg monarchy deeply interested in maintaining control over that Empire. Many Protestant lords side, like the Elector of Saxony, with the Habsburgs, which would seem to show that religion wasn't actually the motivating factor.
But this ignores a lot of context, stripping out the richness and specificity of the history in favor of a clean narrative. One is the backdrop of the Counter-Reformation, during which the Ferdinand II, as Archduke of Austria, was able to roll back the great successes of Protestantism, primarily Lutheranism, that had swept through a substantial majority of the lower Austrian nobility. Through threats of violence and other means of coercion, these Protestant nobles were either converted back to Catholicism or forced into exile. The Bohemians, who had an even longer tradition of rejection of the Catholic Church due to the Hussite Wars (with its practitioners called "Utraquists") and therefore was almost entire non-Catholic after Lutheranism and Calvinism spread through the nobility, were rightly terrified that they were the next targets of the Counter-Reformation as Ferdinand II was poised to replace his fellow Habsburg Matthias as Holy Roman Emperor and the King of Bohemia.
For his part, the Winter King Frederick V was a Calvinist, and was deeply motivated by millenarian ideas about "true" reformed Christianity finally defeating the vile popery of the Catholic Church as a sort of holy monarch. He genuinely felt that he was going to play a key role in the defeat of Catholicism, and the fact that he would become the most powerful man alive in the course of pursuing that aim was only what was natural and necessary. His beliefs seem even more genuine when considering just how out of touch with the political and diplomatic realities of his position, and led to his humiliating summary defeat at the hands of the much stronger Habsburg within a year of the start of his rebellion against them in Bohemia. Unfortunately for many millions, that summary defeat only served to further break the fragile peace between Catholics and Protestants that held in the Holy Roman Empire after the Peace of Augsburg.
This is not to say that everyone was primarily motivated by religious beliefs. France, by then a fully Catholic country again and with a foreign policy determined by a Cardinal, entered the war *against* their own co-religionists in order to prevent the Habsburgs from becoming too powerful. This purely political move almost certainly saved Protestantism on the Continent from utter defeat and mass forced conversations not too long after it had been effectively purged from France.
In short: the Thirty Years War aptly combined political ambition, the dance of great powers, and genuine religious fervor into a horrific tragedy of a war that, by its end, de-legitimized the very idea of a war between Christian sects in Europe. The Thirty Years War was so driven by true religious consideration that, for most of those powers who entered the War, that the Peace of Westphalia was explicitly constructed to prevent such powerful motivators from unleashing war on the continent again.