The difference is we made up a third of the country then. So while it was true that there were people who voted against JFK because he was Catholic, there were a fair number of normally Catholic Republicans who voted for him solely because he was Catholic.
The thing with the Mormons is, they are almost all concentrated in a handful of states and none of these states are really competitive at election time. On the other hand, people who don’t like Mormons are spread throughout the country and they would come out of the woodwork to vote against a Mormon candidate. Especially when a light was shone on the church.
Good points.