"I am not the Catholic candidate for president. I am the Democratic Party candidate for president who also happens to be a Catholic. I do not speak for my Church on public matters – and the Church does not speak for me...."

The reason JFK went in to all that was because people thought the Vatican would have power over a Catholic president. He never said he was forsaking his beliefs or would stop going to church or praying. If he was a true Catholic then his moral code would be aligned to those teachings and influence him in some way or another. This isn't even a bad thing, now if he was talking to god and getting replies back and acting on them that would be a bad thing.