This can be traced all the way back to the Puritans in the 17th century and the bad reaction to the liberties granted to the Catholic Quebecois by the British government in the 18th century. England was a Protestant country by the time it spawned the fathers of the Revolution, and many of the religious minorities were themselves radically moreso.
Agreed. The first colonizers of the United States were either Anglicans who opposed Catholicism or
English dissenters, many of whom were even less tolerant of Catholicism. Even in Maryland, which was founded by a Catholic English lord, the Protestants formed a majority of the colonists. England became somewhat more tolerant of Catholics after the Glorious Revolution (so long as they weren't in line to the throne), but the Thirteen Colonies ironically viewed any attempt to require religious toleration in the colonies as a form of tyranny.
This anti-Catholicism remained a huge force in politics until at least the 1920s, when the KKK was almost as anti-Catholic as it was anti-black. Anti-Catholicism finally died down a little after immigration declined in the period between 1924-1965. By the 1980s it wasn't really a factor anymore, and now we have a Catholic majority on the Supreme Court.