I am not sure where are you getting your info, but if you have visited Chichen Iza, Coba, Tulun... they are mostly all of the original Mayan and other races (as native as it gets). If you look at most Mexicans and some Spaniards, you will find that they are mostly different.
You may be confusing Latin America with North America in which effectively the natives were obliterated and the few remaining live in reserves.
I get all my info from AI - I just don't bother to post their search source. I read and summarize. Chichen Iza was gorgeous (see pic where guy on left stopped so he wouldn't get in the way lol) - and it is one of the larger native areas
According to the 2020 Mexican census 65% of Yucatán’s population self-identify as Indigenous, compared to just 23% of the Mexican population.
I didn't follow the thirty year plight of the "cowboy vs indian" drama, but I do know whether they were pushed into reservations, priced out of their land (like in HI) or just recovered slowly, every native population in America, as well as the thousands of languages they spoke, lost 90%+ of their population in the first century.

Look at Brazil - no jungle, easy agriculture - natives make up only 2% of the population there. I would assume that the Iza area was too bothersome for Europeans to colonize.
