This is a simple question with a complicated answer, because there are varying degrees of, and reasons for, animosity between any two religious groups. This particular battle is rooted in history. Degrees of reaction have ranged from friendly disagreement (as reflected in the numerous ecumenical dialogues produced between the two groups), to outright persecution and murder of Protestants at the hands of Rome. Reformation teachings that identify the Pope as the Beast of Revelation and / or Roman Catholicism as Mystery Babylon are still common among Protestants. Clearly, anyone with this view is not going to “warm up” to Rome any time soon.
For the most part, today at least, most of the animosity comes from basic human nature when dealing with fundamental disagreement over eternal truths. Passions are sure to ignite in the more weighty matters of life, and one's faith is (or at least should be) at the top of the heap. Many Protestants think Roman Catholics teach a works-gospel that cannot save, while Roman Catholics think Protestants teach easy-believism that requires nothing more than an emotional outburst brought on by manipulative preaching. Protestants blame Catholics for worshipping Mary and Catholics think Protestants are apparently too dull to understand the distinctions Rome has made in this regard. These caricatures are often difficult to overcome.
Behind the particular disagreements over the role of faith and works, the sacraments, the canon of Scripture, the role of the priesthood, prayers to saints, and all the issues surrounding Mary and the Pope, etc., lies the biggest rift between Roman Catholicism and Protestantism: the issue of authority. How one answers the authority question will generally solve all the others. When it comes down to deciding a theological issue about defined Catholic dogma, there isn’t really much to discuss on the Catholic's side because once Rome speaks, it is settled. This is a problem when trying to debate a Roman...
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