The United States is seeped in the British experience. As the US developed, its understanding of religion often became a binary. And this is partially because the United States was a slave society that often viewed race as a binary.

In the most simplistic terms, and I’ll get more specific in a bit, the original Europeans to come to the Americas were Catholics. They, along with other Catholics like the French, tended to convert the natives.

The British, used to something of a siege mentality, tended to quarter off areas that were not Protestant and not white and then expand the walls, so to speak. There was, here, a conflation with white Protestants and everyone else.

In New York in 1741 it was widely believed that blacks had been corrupted by the Catholic Irish. There was something of a Protestant version of an inquisition that investigated this conspiracy (which probably didn’t exist) and then, despite terror, torture, and executions, found no evidence of a conspiracy. This did little to reassure the public. And this kind of set the tone. Andy Doolen writes, “This crafted insecurity is our own cautionary tale.” This ongoing “crafted insecurity” was built on racial anxiety and also centered on a Catholic power existing as a counter-American program that promised to upend British colonial society. Protestants viewed Catholics as the root of evil, as “no more objectionable class of people could be imagined.”

In Nootka Crisis of 1790, these lines were solidified as Catholic Spain and Catholic France were looking to go to war with Protestant Britain and the Protestant Dutch.

These anxieties carried into the American Revolution. That history is mostly known, but in Britain and Ireland (where a bunch of immigrants were about to flood the US in the coming century) the Catholic/Protestant binary continued to solidify. After losing the American colonies, Cornwallis went to crush the United Irishman Rising of 1798.

The 1798 Rising was non-partisan, like the US Revolution, but crushing of it was absolutely sectarian.

Though Cornwallis used “the utmost exertions to suppress the folly…of substituting the word Catholicism instead of Jacobinism as the foundation of the present rebellion,” it couldn’t be done. He eventually relented and let the Orange lodges and other very partisan Protestants do what they wished, lamenting, “The minds of people are now in such a state that nothing but blood will satisfy them; and although they will not admit the term, the conversation and conduct point to no other mode of concluding this unhappy business, than that of extirpation.”

These Scotch Irish Protestants and Irish Catholics would eventually come to populate the United States, the same that already had this siege mentality against Catholics.

And this was exasperated going west.

To use my state of Oregon as an example,any of the Natives had already been converted to Catholicism by other Natives that were converted by the French; and many more were open to being baptized by the Jesuits who often dressed like Native holy men, and baptized anyone that wanted to be baptized.

The Methodists wanted to break the back of Catholicism in the Northwest and sent the “Methodist Mission.”

The Methodists, and an increasing number of Protestants, conflated Catholicism with an Old World degeneracy that needed to be wiped out; they also saw a conversion to Christianity as an all encompassing change. The Native, in their view, would give up his “savage” ways, cut down the forests, begin farming, and live as Europeans to show a true conversion. Only then would they be baptized.

The Whitman Mission, the most famous in the Northwest, was active for eleven years and had not found a single Native worthy of being baptized. When Whitman found Natives that were baptized by the Catholic Church, he would react aggressively.

Sideline: there was also a commercial component. American Protestantism was increasingly seen as being tied to private property.

In the case of the Whitman Mission, this meant that when Natives would come and grab things from their garden, they felt justified poisoning the food to teach the natives to not take the stuff. When they wanted to cull the wolves and left poison meat, it was the fault of the Natives for eating the meat they found in the woods. When the Whitmans, after poisoning the Natives in two instances, legitimately attempted to give a measles vaccine to the Natives, they reasonably assumed they were being poisoned and attacked.

The Whitman Massacre was blamed on Catholics. To avenge this, a Baptist named Cornelius Gilliam, who favorably compared himself to the Puritan Oliver Cromwell, went out to destroy the Cayuse people and get to the root of the evil Catholic Conspiracy.

Less known but as relevant was the Cockstock Affair, involving two African Americans and Native Americans in Oregon getting into a conflict about a horse. The Oregon Rangers were established to deal with this and often had a view that the Catholics must be behind the affair.

As time went on there was a general tamper on a lot of these issues as the Civil War came into focus.

After the Civil War, however, the victorious Republican Party expected the urban whites (Jews, Irish, Italians) to come into their ranks. When they didn’t, a sinister fear of the Catholic Church working against them took over. The Nativist movement was brought up again, and again, all Catholics were made suspect.

The basic thrust of this was that many Protestants coming to the New World were looking for a place free of Old World corruption. They arrived to find a continent full of Catholics due to Spanish and French influence, and so set a binary of either being part of their group or an evil Catholic conspiring against everyone else that was a Protestant.

I wrote this on a phone, so apologies if I wasn’t clear enough.

Sources:

Cassandra Tate, Unsettled Ground: The Whitman Massacre and Its Shifting Legacy in the American West (Seattle: Sasquatch Books, 2020)

Elizabeth McLagan, A Peculiar Paradise: A History of Blacks in Oregon, 1788-1940 (Portland: Georgian Press, 1980)

Robert J. Loewenberg, Equality on the Oregon Frontier: Jason Lee and the Methodist Mission 1834-43 (Seattle: University of Washington Press, 1976)

Ohara, Pioneer Catholic History of Oregon (Portland, OR: Glass & Prudhomme Co., 1911) https://archive.org/details/pioneercatholich01ohar

Andy Doolen, “Reading and Writing Terror: The New York Conspiracy Trials of 1741,” American Literary History 16, No. 3 (2004)

Malcolm Clark, Jr, “The Bigot Disclosed: 90 Years of Nativism,” Oregon Historical Quarterly, 75, No. 2 (1971) p. 115 https://www.jstor.org/stable/20613416

I'd actually like to tackle this from a different perspective.

First, to be extremely brief in theological terms: one set of common beliefs that Protestant denominations mostly all share are the "Five Solas": sola scriptura, sola fide, sola gratia, solus Christus and Soli Deo gratia (or: by scripture alone, by faith alone, by grace alone, by Christ alone and for the Glory of God alone). Essentially this means: religious belief should stem from the Bible (not other texts or traditions), salvation comes through faith in God and Christ (not through good works), salvation comes through grace to unworthy sinners (they don't earn it), Christ is the only mediator between God and people (you don't need priests or all the Catholic sacraments), and religious practice should be directed at God alone, not saints or the Virgin Mary.

I'll specify that while these five solas are fundamental principles to almost all Protestant denominations, that's not the same thing as being fundamental to all non-Catholic denominations: Orthodox Churches believe differently. For the purposes of US history we'll put the Orthodox aside as they are a relatively small part of the Christian population, and outside of Alaska were even smaller-to-nonexistent until late 19th century immigration.

Anyway, another piece of context for the United States. One thing to keep in mind is that the United States never had a majority of its population adhering to a single religious denomination. Even at the end of the colonial period, which saw every colony have an official, tax-supported "Established" Church, this was so: estimates via Roger Finke's "American Religion in 1776: A Statistical Portrait" are that for the Thirteen Colonies, about 20% of the population was Congregationalist, 18% was Presbyterian, 15% each for Church of England and Baptists, 10% Quakers, 5% each German Reformed and Lutherans, just under 4% Dutch Reformed, and 2% Methodist. Roman Catholics were 1.7%, and Jews .2% (although we have evidence of individual West African Muslims among the slave population in this period and after, as far as I'm aware no one has actually quantified the Muslim population). So even at this stage, the Thirteen Colonies were overwhelmingly "Protestant", but only in the broadest sense - no single denomination predominated across all colonies, and even when they did predominate locally it wasn't close to universal (for example, Massachusetts was 2/3 or so Congregational). Southern colonies tended towards the Church of England, and New England tended towards Congregationalism, while the Middle Colonies tended towards the biggest amount of local pluralism, to the point that Pennsylvania, Delaware and New Jersey didn't even have established churches (neither did majority-Baptist Rhode Island).

A caveat here is that while (via the Library of Congress) a substantial part of the population attended religious services of some kind (maybe 70%) only 10-20% of the population were church members, ie fully inducted into any one congregation. The point here being that after the American Revolution, the stage was set for a great deal of religious churn - but mostly between Protestant denominations.

So - the American Revolution was not just a political revolution, but something of a religious revolution, especially among the established Church of England (for simplicity's sake I'll call it the Episcopal Church) - clergy tended towards loyalism (as the King was head of the Church of England and clergy swore an oath to him), and this meant that Episcopalians had a great deal of internal conflict. To cut things short, eventually the Episcopal Church managed to work out a situation after the Revolution whereby clergy and bishops could be ordained via Britain, but without swearing oaths to the King (this was codified by an Act of Parliament in 1786), but this whole scenario provided extra impetus for the disestablishment of churches in the new United States. North Carolina and New York disestablished the Episcopal Church in 1776 and 1777 respectively, and Virginia followed in 1786 with Jefferson's Statue on Religious Freedom, which was to be the inspiration for the First Amendment of the US Constitution. The Constitution initially only provided for separation of church and state at the federal level, however, and well into the 19th century New England states had established churches, with Massachusetts being the last to adopt disestablishment in 1833.

It should be obvious that given the religious pluralism in the new US, a lot of other religious denominations were keen to disestablish the "official" churches. But a quick side-track as to why.

The British experience of the 17th and 18th centuries would have informed a lot of their American brethren, but in this context it's important to see that there was not a Protestant-Catholic binary alone. There was an established Church of England - everyone paid taxes for its upkeep, you needed to be a member to hold public office or attend one of the two universities in England, you needed to be married by an Anglican minister to have a legal marriage, etc. Catholics had it worse under the Penal Laws (being banned from voting, bearing arms, severe limitations on property ownership and inheritance, etc), but those major restrictions also applied to non-Church of England Protestants ("Dissenters" or "Nonconformists"), such as Baptists, Methodists, Presbyterians (outside of Scotland, where the Presbyterian Church of Scotland was the established church), Quakers, etc. Their American counterparts after the Revolution were very eager to make sure such discrimination would not be codified in the United States, and these denominations (especially the Baptists) tended to lobby very hard for disestablishment.

Anyway, that is our setup. As we can see, by the 19th century the United States had a pretty thriving religious scene, albeit one where no one single denomination dominated, and where increasingly no one denomination was an official established religion. It's time to introduce Roman Catholicism into the mix...