And let's go way back, long before there were any Protestants you can demonize. We'll see how Rome was already using religion to motivate political conquest and slaughter, centuries before the Reformation. The Pope incited a crusade against "heresy" in Languedoc, the region now considered the south of France, by offering the property of that region to the French who agreed to fight. With the huge wealth of this advanced region dangled before the bloodthirsty, sociopathic warlords of northern France, the result was inevitable: Years of war, about a million dead, and conquest by the French king. All the things you talk about--genocidal massacres, burnings, princelings flip-flopping as conditions changed--happened, and all at the instigation of the Roman church!
This established a pattern which went on and on. His Catholic Majesty of Spain tried to conquer England and force Catholicism down the throats of its people. Did the Pope object? Of course not. The Pope had the nerve to give the entire New World to the pet Catholic powers of Spain and Portugal. When a small colony of Huguenots driven out of their French homeland settled peacefully in Florida, a Spanish force descended on them and massacred the entire lot. You can't find any act by a Protestant nation which compares to the outright genocide inflicted on the Huguenots, a large minority within France, by the power of the royalty united with the Roman religion. Within a few years, Protestantism was almost dead in France. This would have been the fate of Protestants elsewhere, had they not taken up arms and attained alliance with political leaders in Germany and elsewhere. This kind of crap is why our Founders did not want any nationally established church in the U.S.!
The pope did not incite the crusade in Southern France. The temporal rulers had their eye on power aggrandizement and perverted the crusade idea for their own temporal power purposes. The Albigensian heresy was a real threat religiously as well—Dualism strikes at the very heart of the Christian faith. But trying to suppress it by force, in the end, was not wise. The popes who endorsed it were imprudent but the Albigensian crusade was every bit as much if not more a political crusade in its origin and execution.
How to stop heresy is a difficult problem. Let it flourish and people go to hell. Try to stop it by force and you make matters worse. We just say, who cares what anyone believes, which ultimately leads to even worse violence, including the slaughter of innocents in the womb.
We have not solved the religion and society problem today. We opted for religious pluralism, for understandable reasons, but that has led, once the generic Judaeo-Christian consensus faded, to the evergrowing colonization of the public square by militant atheism which is a Culture of Death. You will see horrors unimagined in the past because we have lost any religious consensus upon which to make and uphold public laws. We will have lawlessness unimaginable to people in past centuries.
And it started with an overreaching by the temporal rulers, led by your precious Protestant princes. The legitimate reaction against the overreaching, against the state churches, led to religious pluralism, which was necessary but required careful attention to a lowest-common-denominator Christian-Jewish underlying consensus if it was to survive. It didn’t and now we face the gales of Raw Power with all our laws cut down.