Many people worried about how to prevent such wars from happening again. Jean Bodin had argued that Absolute Monarchy could end the wars by ending political factions. But that still left the question of what religious policy a king should follow. Toleration develops as a way to solve these problems. Locke's Letter Concerning Toleration Separates clearly the spheres of civil society and religion.
Civil society has no concern with religious matters.
The concerns of religion are entirely private, except for public worship. The Church is considered a private society, much like a bridge club or a bowling league. It was the moral compass for the society. With the Enlightenment, this changes. The State becomes the common bond holding society together.