"The same as Catholicism was when Kennedy ran. It won't stop him as the public sees what they are getting."
No, almost all protestant denominations recognize Roman Catholics as Christians. (The reverse is not necessarily true --- many RCs espouse that protestants are going to Hell, but that is beside the point.)
This is a much more serious divide --- many/most protestant groups do not recognize Mormons as Christians at all.
The same groups preach that God provides protection to the US because of its Christian devotion.
They would opine (again, for right or wrong) that God would no longer protect the US if we "turned away."
Etc.
Again, NOT ADOPTING the merits of this argument. Just stating that it WILL OCCUR and will be a very, very powerful argument to a critical portion of the electorate.
In the early sixtys Catholics were considered idol worshipers and not true Christains by many fundamentalists. You are looking at Catholics through todays lense not the prevailing sentiment at that time.
I would hazard to guess that if a similar poll had been taken back then a similar percentage of people would state they would not vote for a Catholic. Romney will educate the public as did Kennedy.