First, consider that the N American continent wasn't as heavily populated as central and S America at that time, with the N American tribes being largely nomadic hunter/gatherers while the central and S American tribes had more advanced and established civilizations that were on the order of the early Egyptian societies, capable of supporting a larger population.
N America has a wider range of natural resources useful to industry: iron, copper, etc..., but those require industrial methods to obtain and refine, so it was more conducive to the industrialized Europeans, as was the temperate climate. Central America was hot, and S America tended to alternate between rain forests and and temperate with very craggy topography, not ideal for industrial activity.
The rising industrialization also drew a lot of European immigrants during the late 1800's and early 1900's. Almost none went to central and S America.
It's not so much that fewer native Americans survived in N America, more that the Europeans heavily populated N America due to industrial growth. This reduced the percentage dramatically, not the overall number of natives, while central and S America didn't see near the population explosion, because the conditions there weren't conducive to industrial development.
As for the idea that the Spanish and Portugese were somehow 'kinder', that ignores the African slave trade. Central and S America were rich in one resource: gold and silver. This may be one reason the central and S American nations flourished: gold and silver are easy metals to refine and work with, well within the capability of pre-industrial societies. A primary reason both metals became the first forms of currency.
And it was the gold and silver mines that consumed the vast majority of Africans in the Atlantic slave trade.
Destination of the ten million Africans taken to the American continent:
Portuguese America 38.5%
British America (minus North America) 18.4%
Spanish Empire 17.5%
French Americas 13.6%
British North America 6.45%
Dutch West Indies 2.0%
Danish West Indies 0.3%
The N Americans of African descent have increased in percentage, to around 11% of the total population. The former British colonies of Jamaica and Haiti are currently populated by people largely of African descent. In both cases, most of the slaves survived and lived long lives.
Yet, in the former Spanish and Portugese colonies, the percentage of people of African descent today is quite low, despite the fact that over 70% of the 10 million Africans brought to the American continent went there.
Why? Because most of them were dead within a year, victims of the harsh conditions in the mines, and the very hot and humid climate where the gold and silver were located. The Spanish and Portuguese had calculated that a slave only had to live one year to return the expense of their slavery. This also accounts for why the vast majority of Africans were taken to Portuguese and Spanish territories: the death rate was so high.
That is an act of genocide, in the five to six million death range, for which the Spanish and Portuguese have never been held accountable. So the idea that the Catholic faith protected people, doesn't hold up when all relevant factors are considered.