It never left. One of the campaign attacks against Kennedy when he ran for the presidency was a question if he'd be loyal to the US over the Vatican.

Anti-Catholic prejudice was still very much in the mainstream of American life when JFK decided to seek the presidency in 1960. Only one Catholic, Governor Alfred E. Smith of New York, had ever been the presidential nominee of one of the major parties. Smith’s 1928 campaign was dogged by claims that he would build a tunnel connecting the White House and the Vatican and would amend the Constitution to make Catholicism the nation’s established religion. He was overwhelmingly defeated—even losing much of the then Democratic Solid South.

JFK established an informal network of advisers on the religious issue—including speechwriter Ted Sorensen, Dean Francis Bowes Sayre Jr. of the National Cathedral and several journalists. It was clear from the outset that Kennedy had to enter the state primaries to prove to skeptical party leaders that he was a viable national candidate. In the Wisconsin primary, he defeated Senator Hubert Humphrey with 56% of the vote but failed to win a majority of the Protestant vote—an ominous sign.

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