I think people believe what they absorb from all sources--from movies to TV shows to history books. The problem is that most people have seen 10 or 100 movies and TV shows featuring stereotypical Indians for every book they've read. If the ratio were reversed--10 or 100 history books for every movie or TV show--I think their beliefs would be reversed too. But that isn't the case.
I'd say this applies to every work of fiction featuring Indians, not just Apocalypto. I've written about it often--in general and in specific cases such as Apocalypto. For example:
Why people believe movies
The influence of movies
Verisimilitude in movies
Audiences don't want dry facts
Others have written about this too because it's patently obvious. Movies try to recreate reality with locations, sets, costumes, and so forth. Lincoln was a tall guy with a beard and a hat, not a short bald woman. If everything else in a movie strives to seem real, why would someone assume the Indians are false and unrepresentative?
Answer: No one would assume that. The fact that is that few if any people think critically about the elements of moviemaking. They assume a Native-themed movie is based on reality because the vast majority of historical dramas are based on reality.
I hope that answers your question. Let me know if you have any other questions.
P.S. For more on the subject, see The Best Indian Movies.