Since I attend a Mexican University, I can give you an answer for this question in the context of the New Spain (the spanish-speaking parts of the American continent). When the Spanish first arrived in the Americas, you gotta remember what the situation was like in Europe: religion was above any King and any ruler. Massive wars had been waged because of Religion. The year Columbus arrived in Hispaniola, was the year that the Spanish finally against the moors, in effect, kicking them out of the Iberian peninsula as they were pretty much heretics for not being of the Christian cult (mainly Catholic, as protestants had not come about for another couple of years [I believe it was in 1517, if I am wrong, please correct me :)], with Martin Luther). Now when catholic priests started arriving in the Americas, they saw pretty much heretic practices: idolatry, polytheism, among other things within the Native peoples of the Americas, BUT! And this is key in understanding, the people of the Americas (as opposed to Africans) were just lost souls who needed to be shown the way of God and Christ as to not suffer damnation in the afterlife. At least, this was the rationale that the Spanish had- they were educating lost souls on the truth of the one and only Christian God. They saw American natives as a kind of innocent infant, if you will, spiritually speaking.

It was also used a means to subdue and repress, and to an extent annihilate an already existing culture, by placing the conqueror's customs and culture upon a people. In theory, the church was the head huncho, and more so a pivotal force in the conquest of New Spain than Hernán Cortés and his 500 men.

I hope this helped clear up any doubts, even if it you were asking in the context of protestants arriving in the 13 colonies and then spreading their gospel some years later.

Cheers.