That would explain all the anti catholic/papal sentiment in America at the time?
America was anti-Catholic because they were mostly Protestant. Same reason Britain was extremely anti-Catholic. America, at least the British colonies, were never under the Pope though, since they were established after Britain went Protestant.
In fact, even the Catholics in the New World (Spain and France, for instance), were not really under the Pope. This much is clear because the Pope opposed slavery (the Catholic Church's opposition to slavery is why it largely died out during the Middle Ages in Europe, replaced by serfdom and other systems, whereas in pagan times slavery was rampant). The Pope issued an official declaration in 1537,
Sublimus Deus, which forbid slavery in the New World. It was completely ignored. The Pope, of course, had power in Europe which backed him: the "Holy Roman Empire". The Emperor (who was also the King of Spain) issued the Leyes Nuevas in 1542, which gave some teeth to the Pope's words by making them official force of law. However, they were still largely ignored. Therefore the Emperor sent over a Viceroy to enforce the laws in 1546, one Blasco Vela; unfortunately, when he tried to end slavery by force, the Conquistadors just killed him and paraded his head around on a pike. The Pope at least eventually brought about the abolition of the slave trade however, but that wasn't until the early 1800's, under Pope Pius VII.
So, as you can see, the Pope had little to no power in colonies that belonged to Catholic states. You can be entirely sure he didn't have
any power over colonies that belonged to Protestant states.