The 16th-century split between Catholics and Protestants was a source of vicious animosity among Christians and fueled major conflicts in early modern Europe — persecution, rebellion, assassinations, massacres and of course the exceptionally destructive Wars of Religion.
From what I can tell, evidence of a continuing Catholic-Protestant divide survived well into the 20th-century. Maurras listed Protestants as one of the four pillars of anti-French subversion. Ownership of a Protestant Bible was illegal in Francoist Spain. It was frequent for Catholic and Protestant children to attend different schools in Canada. Catholics were officially barred from public employment in Sweden and Norway until the '50s.
Still, that's a long shot from the St. Bartholomew. And nowadays, Catholic-Protestant conflicts are largely a forgotten thing of the past in Europe — with the complicated exception of Northern Ireland. Europeans identifying as Catholics or Protestants generally see each other as fellow Christians, not as traitorous hellspawns... at least as far as I can tell.
What, exactly, caused the century-long enmity between European Catholics and Protestants to fade over time and eventually to largely disappear? Did key events cause a dramatic decrease in conflict, or was it more gradual and haphazard a development? Did the emergence of the modern nation-state create an incentive to move beyond Catholic-Protestant enmity, at least wherever they shared a territory?
Note: I am focusing on Europe explicitly because I understand that while anti-Catholicism is nowhere near as hegemonic and aggressive as it used to be not so long ago in the US, it is still very much a somewhat marginal phenomenon. Though interestingly enough, it was abandoned by one of its historical standard-bearer, the Ku Klux Klan, in favor non-sectarian white supremacy.
In essence the question was settled by the Peace of Westphalia in 1648 which concluded the 30 years war.
After 30 years of war that carried some implied religious animosity, it was not entirely a religious war as it sometimes is called (nor about Habsburg power, more properly option C) all of the above). However, the question of religion and how it related to temporal issues, i.e,. who could lay their hands on church lands (after tough negotiations the status of the year 1624 was agreed upon for deciding which lands remained secular and which were returned to the Catholic church) played a significant part in it's start, but was also specifically addressed in the peace treaty. So the interpretation that wants to completely ignore the religious aspect also misses the mark (this is usually where it's called an anti-Habsburg war). The previous wars of Religion, not only in France, but in the HRE likely also featured in the thinking.
The peace treaty affirmed that the earlier agreement of the Augsburg peace of 1555 would hold. This allowed the princes of realms within the Holy Roman Empire to choose what religion their subjects had, or rather define what the official religion was. It extended this, however, to also recognizing Calvinism as an equal option together with Lutheranism and Catholicism. Furthermore, it stipulated that those who did not follow the creed the prince decided on could not be forced to convert and were allowed to practice worship in private as well as in limitedly in public (by allotted hours). So it's not complete religious freedom, but sort of an "you can worship as long as you don't make a big deal about it". If you did not wish to remain in a principality which did not share your religion you were guaranteed the right to emigrate.
All of this to a large degree defused the religious tension into a tacit acceptance that war couldn't change the religion and that the Western church was now permanently split into factions.
In essence it removed religion off the table for reasons to go to war in Europe. Mostly. It also somewhat eased the tensions of co-habitation of religions in that many started relocating to areas more agreeable to their confessional choice. Though e.g. in France not exactly voluntarily, though those within the borders of France were not part to the treaty anyway. Though the Catholic counter-reformation mostly stopped at the peace treaty we do get a situation where Protestant countries become more protestant and Catholic countries more catholic.
Basically this massive discharge of violence that was the 30 year wars stopped outright massacres and re-converting by the sword in Europe more or less. After this, while mistrust existed, the lines of conflict were never really neatly draw along the lines of religion again. And nations learned to adopt a more realpolitik approach to their dealings rather than hardline ideology. It didn't happen overnight of course, but removing religion as motive let cooler heads prevail and wars could be fought for more rational reasons. If such a thing could be said of wars of course.
Ever inventive of course us Europeans then promptly invented nationalism as a way to separate the "us" and "them". But that's a whole another two wars.