Lots of early modern English history was shaped by religious conflicts-- after Queen Elizabeth appeased a new Protestant majority by making the Church of England officially Protestant she fined catholics and denied their access to many things. She also revoked all of the Pope's political authority. When Catholics ruled the land both before and after Elizabeth's reigns, the same was the case for Protestants.
Fundamentally, they hated each other becausea) they believed god was angry with their country and countrymen for allying to the wrong religionb) for Catholics the pope should be an important political figure, whereas the Protestants really disliked himc) many Christian traditions were split between the two groups and both wanted their own to be part of the law