Latin America is an extremely complex place. On one hand, yes, being called an Indian is pretty much an insult and yeah, the more pure Indians are at the bottom of society. On the other hand, most will gloat about how great and wonderful the Aztecs and Incas were. And mestizo pride is pretty mainstream and accepted, which is like a built-in acceptance and pride in indigenous culture.
And yeah, the Caribbean natives were almost wiped out but not entirely. I read somewhere where they did a genetic study of Cubans, Dominicans, and Puerto Ricans and while they had little indigenous in comparison to mainland Latin Americans, it was more than previously thought. Puerto Ricans actually had the most at around 15%, I believe.
Just looking at some Puerto Rican celebrities, you can see a noticeable amount of indigenous, even though they're mostly black and white.