mohe:
JFK's Catholicism was controversial all over the South, among other places, that is why his victory in the West Virginia primary was so signifigant, until he won there even many prominent Catholic politicians such as Pat Brown, the very catholic governor of California, would not support him because they were almost certain a catholic could not be elected President. When Kennedy won WV they all came around with great enthusiasm.
The similarity between this and the number of black leaders today who seem chary of Obama for almost identical reasons is quite striking.
You have to remember that throughout the 1800s the Catholic Church opposed democracy and religious freedom. The Church taught that it was every Catholic's duty to work to establish Roman Catholocism as the official state religion and to support Catholic kings who could impose Catholic policies.
We no longer care about Catholic politicians because today's Pope doesn't preach this, and even if he did, most Catholics would not pursue it any moreso than they obey his dictates on birth control.
But it was not always like this. (Even JFK's father and brother had enough obedience to refrain from using birth control; it was not obvious where they would draw the line.)