The beef with marrying Catholics in particular is because it was an issue that they thought (in the immediate post-Reformation era) that the primary allegiance of a Catholic would be to the Pope, and in turn, potentially with the monarchs of Catholic countries like Spain. Catholics were viewed as traitors.
I was amazed to find out what a huge deal this fear by Protestants of Catholics was. I've just finished "The Watchers" by Stephen Alford - the history of the Elizabethan secret service under Frances Walsingham.
Of many amazing facts, I discovered that when Elizabeth's spies uncovered the Babbington plot to remove her and replace her with her Catholic half-sister Mary, Elizabeth personally countermanded the instruction for the Catholic plotters to undergo the usual punishment for traitors of being hung, drawn and quartered (already pretty gruesome) and instead insisted on the construction of a specially designed public scaffold, so that the limbs of each traitor could be torn off their torso while still alive. Nice.
P.S Reading into the history of faiths in Europe and their purpose in shoring up or tearing down political power must be the surest way to turn anyone with any remaining doubts into an atheist.