What acts of violence have Catholics and Protestants inflicted upon each other in Ireland?

Are you talking about the crusades, Or are you talking about things more along the lines of the inquisition? Either way, protestants left the pope for these reasons, among others and generally arent aggressive to non-believers. This explains the early stages of violence between the native Irish Catholics and the Scottish and English "settlers": http://en.wikipedia.org/wiki/Irish_Rebellion_of_1641#Ulster_Massacres