It’s worth remembering that most of them were killed by disease, and that the diseases travelled faster than the colonists. Europe had had centuries of people living in filthy cities where all kinds of diseases were constantly breeding. The survivors carried those diseases but were immune to them. As soon as they met the native populations, the natives were exposed to countless deadly diseases that were completely new to them.

Now, sure, the colonists went and tried to slaughter as many natives as they could, but often they’d get to a new native settlement and find it was mostly empty because everybody had already either died or fled. Who knows, the natives might have been able to put up a fight against the colonists if they hadn’t been so devastated by the diseases. I’d bet that the colonists just took all the natives dying as another sign that their conquest was blessed by their god.