I think the answer to your question lies in this quote, which appears on screen at the beginning of the film: "A great civilization is not conquered from without until it has destroyed itself from within." ~ W. Durant
In the middle of the film, when the captives are being led through the city, everything they see around them indicates a decadent civilization in decline. Their crops are rotting and being eaten by bugs, there's a plague ravaging the outlying areas, people are starving on the outskirts of the city while the spoiled, overdressed gentry sit around in the streets looking bored and disgusted with everything when they're not bartering for slaves, and the people are putting their trust in a corrupt king and a shifty priest who claim they can fix everything (and cause solar eclipses) by tearing people's hearts out and rolling their severed heads down the temple steps. The implication seems to be "Yeah, Europeans arriving was bad for the natives, but the natives had let themselves become pretty corrupt and evil by that point anyway." How fair or accurate that might be is a question for more learned men than me, but that seems to be what they're getting at.
Whatever the film's message (implied or otherwise) might be, it's really just background noise to the main story. The real focus is Jaguar Paw and his quest to get home and save his wife and kids. It's a similar situation to Neil Marshall's Centurion - that film shows evidence of both warring sides (Roman and Pict, in that case) being absolutely awful, which leads some people to argue about which side they're supposed to be rooting for. The answer is, of course, neither. You're supposed to root for the small group of characters stuck in the middle of it all. If you don't mind a spoiler, the film ends with a Roman man and a Pict woman, both exiles from their own people, settling down in the woods and finding happiness with each other. Apocalypto ends with Jaguar Paw and his family going off into the jungle to "seek a new beginning", basically turning their backs on the decadent Maya and the soon-to-be-conquering Spanish as they go.
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