I read an article about the Stono rebellion in South Carolina in 1739 which argued that the slaves were Catholics (captured in the Angola region) and were trying to get to Spanish Florida.
I think the notion of toleration for Protestants of different types, but not for Catholics, may be drawn from John Locke's essay on toleration, written about the time William and Mary extended toleration to Protestants in Britain (although there continued to be disadvantages for non-Anglicans).
One of the reasons for the intensely negative reaction to the Quebec Act of 1774, I think, was that it gave rights to the French Catholics in Canada. Of course they also didn't like the enlargement of Quebec to include the land north of the Ohio River.
The King of Spain crammed down the treaty. Before that NO Europeans other than the Spanish and Portuguese had privileges of settling in the Americas.
People tend to forget that Spain won the war, had all the money, owned all the land, and an enlightened king (Philippe II/III) had a large number of Protestants to rule throughout his Hapsburg realms ~ and his solution was to give them somewhere else to go ~ imagining that this would lead to peace in Europe.
He got 20 years of peace. Then the item called "The Thirty Years War" happened.
My own French ancestors who lived in that land North of the Ohio were Protestants ~ they also had relatives along the Green River in Kentucky. Those settlements go way back into the early 1700s. Prior to that, the Spanish control of that part of the world was more nominal than real.
When the American Revolution started those folks adhered to the American cause. The proposed "new nation" had not signed any treaties with Spain although very quickly Spain became an American ally in the war. France took a bit longer. Nederland, Denmark AND Turkey (Ottoman Empire) extended recognition almost instantly. I think that was the beginning of the entity we now call NATO.
The Treaty of Paris that concluded the Revolution left Spain in charge of everything West of the Mississippi, and along the Gulf Coast (including Florida). England kept Canada. The former French territories North of the Ohio were yielded to the United States but with British forts to protect the fur trade (ha, ha, ha!).
The two biggest items were that France was squeezed out of America ~ even their oldest claims were exterminated, but the United States, their ally, was put in charge of Philippe II/III's Protestant ghetto. That opened up that vast territory with its resources to French business interests ~ which was all they ever really wanted.
We are all familiar with history since that time. Toleration for Catholics was extended into the United States and Canada, and after Mexican Revolution, toleration for Protestants was extended gradually into Latin America.
Sometimes folks forget that neither the Spanish territories nor those they granted to France, and to other Europeans for settlement, started out in a state of religious or political toleration.
However, if you read that old Treaty of London 1604, toleration is in there ~ provided you did not publicly "offend" the ruling party.
That was a major advance in the history of Europe ~ just short of the Edict of Nantes, but it was something. In fact, the question of whether or not Spain (aka Hapsburg Empire) itself could allow its citizens to practice their own religions in private was not settled until the conclusion of the Thirty Years War and the Peace of Westphalia.
Whatever English political philosophers thought about it, the practices on the ground in America were far more liberal than imagined in Europe. The Puritans didn't really take over Maryland ~ Marylanders took over Maryland. By the 1680s everybody here had cousins who were Catholic and cousins who were Protestant, and not all Anglican. They were a very intermarried bunch (although marriage was pretty much a private matter controlled by families and not the government). The Catholic Carroll family might well not have a good title to their farms but their Protestant Carroll cousins took care of that. Later on as the Ohio Country and Kentucky were opened up the families clustered around St. Mary's Maryland set up their own "colonies" made up of both Protestants and Catholics from throughout Southern Maryland. The girls still get sent back to St. Mary's for college, and marriage and intermarriage continues apace.
My Great Great Grandmother Mary Ann Elizabeth Smallwood Murphy could certainly attest to what happened.