It seems like the Native Mexicans (for lack of a better phrase) assimilated with the Spanish so that today a large majority of Mexicans are "Mestizos", people with varying degrees of Spanish and Native Meso-American ancestry.
Why didn't that happen with Native Americans?
Or why did it happen with Native Mexicans but not Native Americans?
More could always be said, but you might want to check out this section of the FAQ.