The wars between Catholic and Protestant were mostly over the Authority of the Pope - who had become in effect Emperor of the World during the wars to push back the Moslem conquest of Europe ("Crusades"). The German princes seized on Luther as a religious leader to gain the support of the people to rebel against the Pope - this was more of a political than a theological issue.

Other issues resulting in localized violence was persecution of the Anabaptist sects. These did not believe in infant baptism, and their members were rebaptized. This was seen by mainstream churches as claiming their baptisms were invalid (kinda true). Heresy (perceived or real) often gained a death penalty. Sadly, even this was not a deep disagreement. Catholics first dealt with the death of martyrs under Roman persecution before baptism by proclaiming it a "baptism of blood". Then what about still born babies, or infants who died before baptism. If the parents intended to baptize the child, this was called a "baptism of desire". Anabaptist believers intended to baptize their children, and did so when the child could communicate their desire to do so. This is in effect a "baptism of desire".