I don't agree with the premise of your question.

The 2010 Census indicates 685,150 individuals who self-identified as Hispanic also self-identified as American Indian/Alaskan Native alone. True, they are the minority compared to the 2.2 million who self-identify as American Indian/Alaskan Native alone who also indicated they were Not Hispanic or Latino, but the long-term Spanish colonial presence in North America only extended to a few U.S. states. We need to examine the patterns of self-identification in a state with an extended period of Spanish colonial influence to see how many Hispanics/Latinos also indicate they are American Indian.

In New Mexico, for example, 10% of individuals who self-identify as Hispanic also self-identify as American Indian/Alaskan Native alone (17,854 out of 175,368). In Arizona 15% of Hispanics also self-identify as American Indian/Alaskan Native alone, and in California the majority of people who self-identify as American Indian/Alaskan Native (200,551 out of 362,801) also self-identify as Hispanic/Latino.

The 2010 Census data indicates that many Hispanics, particularly in the U.S. Southwest, do indeed self-identify as American Indian or Alaskan Native. It is important to remember, though, that self-identified race is a complex indicator subject to influences from multiple sources. Genetic ancestry, cultural context, societal classifications, and perceived tolerance/intolerance all influence how we label ourselves.

Could you clarify a bit? Are you talking about people with both Hispanic and native North American heritage?

Well, their cultures were all but destroyed by the Spanish colonists that took hold. I assume you're talking about Latin American people (Mexico and below) and not people from the tribes further up North (Spain didn't colonize these areas so their not Hispanic, but the tribes we would normally refer to as "Native Americans" or "Anerican Indians".) Anyways when the Spanish started to colonize in the 1500's, they were not at all kind. They set up the encomienda system that placed thr native populations at the absolute bottom in the social hierarchy. The natives were rounded up and used as slaves much of the time, and many of them died from European diseases that they weren't immune to such as smallpox, dyptheria, hay fever, typhus, pulmonary plague, etc. Vast amounts of Natives were killed by disease, with percentages fluctuating from high to higher, some tribes being wiped out entirely.

One example of Spanish brutality would be the implementation of the Mita system. In Potosi, in Bolivia, the Spanish re-arranged the mita system that the Incans put in place. The Incans set this system up where every man who was able to sustain manual labor, got a certain amount days set aside every year to work on infrastructure for the Incan empire such as roads, highways, bridges etc. The Incans were flexible, making sure you had enough time to care for your family and own personal issues, and not spend to much time laboring over public works. When the Spanish came in, they re-worked the whole system into their favor. The Spanish forced most of the people who worked under the Mita system into mines, as there were vast silver deposits in bolivia. These men were forced to work tirelessly, in dangerous conditions where bad air and cave-ins were not uncommon. The miners were frequently abused and beaten by spanish over-seers. The workers were forced to pay for food with money they didn't have, and set up a debt trap, where no miner was capable of leaving the mines unless he paid off his debt, meaning the mines were somewhat if a kingdom-come. Once you're sentenced to the mine, you won't make it out alive.

European diseases, mass desecration of temples and religiously significant objects of worship, and overall subjugation and abuse of the Native population led to a marked decrease in Native culture. Any natives that survived the spanish brutality were converted to Christianity, essentially making it so that the Spanish replaced Native American cultures and religion with that of their own. That is why there are very few Hispanics that identify with their Native cultures, cause the Spanish colonists tried their best to destroy the indigenous culture and replaced it with that of their own.