The fact remains that the Catholic Church was anti-republican until the second Council, and that the Catholic clerisy was traditionally politicized, which was antithetical to the founding ideas of this country. Now if you want to talk about discrimination against someone simply because of their religion (and I'm talking about individuals here), then yes, Catholics were unfairly targeted, along with Jews and Mormons. Nevertheless, the urban political machines that arose in the late 19th century were largely Catholic institutions. Moreover, I cannot fault the founders and other Americans of the 18th and 19th century for being suspicious of Catholic influence contra our Enlightened Republican form of government.
BTW: The increase in influence of the protestant clerisy during the second and third Great Awakenings was also greated with horror by true republicans. Religious belief was a right left to the people, but clericalism itself was a cancer to be fought.