Actually, European diseases did most of the work in places where the population was decimated.
I spent a considerable amount of time in New Mexico, and the thing that suprised me is that the Indians I met didn't really like us "northeners", but they REALLY didn't like the Hispanics.
Thanks to the spread of the Spanish black legend by American textbooks influenced by Protestantism for 150 years. The Indians were wards of the government, and the government was determined to make the Protestant Christians. Spitting on the Spanish Catholic period was necessary to do that.
Abuses in colonial management and conquest happened both with Catholics and Protestants. It would be hard, if not impossible, to nail down who committed the most atrocities.
We aren't playing atrocity one-upsmanship here. We are pointing to the difference between the Spanish-Portugues-French areas, where there are large numbers of native Catholics, and the Protestant areas, where there are almost no natives.