In the century after Luther's theses, Europe killed its way through the question of whose Christianity was correct. The German Peasants' War. The French Wars of Religion (eight successive civil wars between 1562 and 1598). The Dutch Revolt against Spain. The Thirty Years' War (1618–48), which killed perhaps a third of the German-speaking population. By the time the smoke cleared at Westphalia, Europeans had concluded — exhaustedly, not philosophically — that living under a different denomination from your prince was preferable to extermination.
The wars of religion are the canonical case for the proposition that the modern liberal toleration of religious difference is a political solution to a military problem, not an ethical achievement. After the Thirty Years' War, no major European power ever again committed itself to wholesale war for confessional reasons; the costs had been too obviously unsupportable. Toleration entered first as pragmatic mutual recognition between Catholic and Protestant princes and only later, slowly, as a positive value extended to dissenters within each state. The St. Bartholomew's Day Massacre, the sack of Magdeburg, the witchcraft persecutions, the long Catholic-Protestant border violence in the British Isles — these are the events that secular liberalism is, in retrospect, an insurance policy against. People who think religious toleration is fragile in the modern West are correct, but the fragility is built in: it was an exhausted truce, not a metaphysical settlement.
Every contemporary debate about religious accommodation, secular public space, and the rights of minorities sits on a substrate that was built out of a century of European blood. The substrate is not as durable as we sometimes assume. Sectarian violence has not disappeared from history; it has only relocated.