When we get back to colonial America, perhaps the most prevalent persecution (both cultural and legal) was against members of the Roman Catholic Church. Marian T. Hovart—a Catholic historian, journalist, and author—once described the era between 1645 and 1763 as the "penal era" for Catholics in America.

Citing a collection of eighteenth century quotations and sources compiled by Sister Mary Augustina Ray in 1936, she talks about a general anti-Catholic sentiment prevalent in America brought over from Great Britain. Rhode Island passed laws that restricted Catholic, Georgia promised religious freedom to all people "except papists," Massachusetts Bay colony passed a law promising the death of "all and every Jesuit, seminary priest, missionary or other spiritual or ecclesiastical person made or ordained by any authority, power or jurisdiction, derived, challenged or pretended, from the Pope or See of Rome," and even Maryland—the original Catholic colony—was overtaken by Anglicans and passed harsh restrictions on Roman Catholics practicing their faith.

Toward the time of the revolution, states like Maryland and Virginia passed freedom laws to ensure all people the right to free religious practice and in the army, General Washington attempted to put down anti-Catholic sentiments.

If we want to look at justifications, we have to look to the anti-Catholic sentiment that had come from the Anglican Reformation in Britain. The reformation itself created a strong sentiment of anti-Catholicism as the Church of England became linked with the everyday life of the average person living in England. Robert Curran in his book Papist Devils wrote "To be English was to be anti-Catholic."

America having been a British colony and heavily influenced by British culture, it makes sense that this sentiment would've carried through into American culture.

Sources:

-Marian T. Horvat, "Let None Dare Call it Liberty: The Catholic Church in Colonial America," Tradition in Action: (2006), accessed September 14, 2016.

-Paul F. Boller, Jr., "George Washington and Religious Liberty," The William and Mary Quarterly Vol. 17, No. 4, (1960):, pp. 486–506.

-John Tracy Ellis, American Catholicism, (Chicago: University of Chicago Press, 1956).

-Robert Emmett Curran, Papist Devils: Catholics in British America, (The Catholic University of America Press, 2014).