It is true that the Caribbean Indians did not all die but the numbers were reduced to such a degree by diseases that their numbers made it impossible to survive as a distinct people.
In Spain itself, Catalonia had been ravaged by the Black Plague introduced from the East so that it's population had gone from 430,000 in 1365 to 278,000 in 1497. The population was large enough, however, to allow the survival of Catalonia as a distinct people, both biologically and culturally. Today, the Catalonian language is important enough to even has it's own Yahoo site.
In Puerto Roco, however, the Year 1771 census was as follows:
Whites...............31,951
Indians.............. 1,756
Free Colored.........24,164
Free Negroes......... 4,747
Mulato Slaves........ 3,343
Negro Slaves......... 4,249
Today, many Purto Ricans style themselves as "Tainos" and it is true that, if you go back far enough, a certain percentage have some indegenous Indian ancestors. However, their Taino bloodline can only be evident by DNA analysis and the "Tainos" no longer exist as a visually or culturally recognizable people.
By contrast, in Mexico, the visually evident racial appearance is predominantly Mesoamerican Indian.