The battle lines between Protestantism and Catholicism were firmly set by the 1560s. The Catholic Reformation established Catholic orthodoxy and launched a massive, and largely successful, campaign to re-affirm the loyalty and enthusiasm of Catholic laypeople. Meanwhile, Protestant leaders were equally hardened in their beliefs and actively inculcated devotion and loyalty in their followers. Nowhere was there the slightest notion of "religious tolerance" in the modern sense - both sides were convinced that anyone and everyone who disagreed with their spiritual outlook was damned to an eternity of suffering. The wars of propaganda and evangelism gave way to wars of muskets and pikes soon enough.
Image Citations (Wikimedia Commons):
Council of Trent - Public Domain
Ignatius of Loyola - Roy Sebastian
The Ecstasy of St. Theresa - Napoleon Vier