This is a statement from my Latin American teacher:
The racial questions is really complex in Latin America and it is very difficult to generalize. In some ways Latin Americans are less racial than other areas (the United States for example) – Latin Americans have historically been more willing to miscegenate. But in other ways a deeply rooted racial problem persists and you will definitely see hostility toward people of darker color in many areas. It is no coincidence that the “elite” and wealthier classes in most regions of Latin America tend to be lighter skinned and many are direct descendants from Spain. At the same time people of color, indigenous, and darker skinned mestizos make up a majority of those living in poverty. That can be partially explained by racial attitudes but not completely. Remember that historically darker skinned Latinos have made up the underclasses and there have been few institutional changes that would allow people to move easily out of poverty (regardless of their color).
The example you gave from Puerto Rico and the Dominican Republic is a complex one that may partially be explained by feelings of racial superiority. But I would argue that we should also consider the nationalist issue. Latin Americans often jealously guard their nationalism, particularly against other Latin Americans and they look for things that set them apart from their neighbors. Sometimes it is race that sets them apart but it often goes much deeper.
Some links with similar topics:
The Last Puerto Rican Indian by Bobby Gonzalez