Catholicism has often been seen as a religion that is fundamentally opposed to American values. There have been times in American history when there were political parties that had anti-Catholicism as important parts of their platforms. The mid-1800s was one of these times as the "Know-Nothings" warned of the dangers of Catholicism.
The reason for this was the fact that Catholicism was such a hierarchical religion with a strong authority at the top. Know-Nothings felt that Catholics would be obedient to the Pope, a foreign authority. They also felt that Catholics were not properly democratic because they gave their allegiance to a figure who was essentially like a king.
Because of this, many Americans felt that Catholics threatened the American "project." They threatened it because they were obedient to a "king" who was not American.