One should consider the acknowledged influence of Mel's dad, Hutton Gibson. They are ideologically joined at the hip.

Mr. Gibson Senior is said to be an "expert" on "The New World Order."
Basically, Gibson, and especially his father, are both somewhat obsessed Catholics that are very much against what they see as our decadent and misguided contemporary culture. Appocalypto is a heavy-handed, cultural critique of today's Western society, especially its pernicious cities.This critique also comes with a prophetic warning regarding "The New World Order." Gibson uses (misuses) Mayan and tribal cultures as a symbolic trope to highlight the government/private sector dichotomy: immoral, greedy government city vs. family-oriented self-sustaining kin group. Gibson doesn't need to be historically or ethnographically accurate with his use of Mayan civilization. He wants to make a point.
Let's listen to his father:
"We're going to have to do something now in this country
because that government is useless. There's a line the
Declaration of Independence where somebody abolishes
or sets aside or misgoverns, it is our privilege the constitution,
it is the people's obligation to abolish that government. I think
there is a way... There is a bloodless way to do it if we can
swing it: secession. Just get all states to secede from the
government and leave it there high and dry. The alternative
is eventually they are going to clamp down on us and we are
going to have the same terror and we are going to have to
revolt with a gun or we are going to face the same (governmental)
terror...We're going to have to do something fairly soon,
because the longer it goes, the more power they get and
the less we have."
It's easy to see how Apocalypto uses the great Mayan city as a symbol of government power run amok. They need sacrifices (taxes) to keep going, and they prey on the innocent (villagers minding their own business) to get what they need to maintain their immoral society. It's actually quite obvious what the Gibson's are trying to tell those willing to go see his work, another reason Mel funds his own movies of late; he controls the message.

These are the "good" villagers who've yet to be absorbed into the evil city.

The evil Mayan city with its overlords (government).
So it should not surprise anyone that Mel and his dad simply "use" Mayan culture to make a point about the coming "New World Order." But some anthropologists and archeologists feel obligated to point out the flaws in their depiction of Mayan culture:
"First, a typical Maya village is shown as an unorganized
group of jungle people who appear to subsist on hunting
alone. The Maya were an agricultural people with a very
structured social and economic system. Even small villages
in the hinterlands of large cities were connected to some
political center. The jungle people in Gibson's movie are
flabbergasted at the sight of the Maya city, exclaiming that
they have never seen such buildings. The truth is, pyramids
of comparable size were never more than 20 kilometers
away from anywhere in the Maya world, be they occupied
or abandoned.
Second, Mayan city people are shown as violent extremists
bent on harvesting innocent villagers to provide flesh for
sacrifice and women for slaves, leaving the children to die
alone in the jungle. Hundreds of men are sacrificed on an
Aztec-style sacrificial stone, their headless bodies thrown
into a giant ditch reminiscent of a Holocaust documentary
or a scene from "The Killing Fields." Problem is, there exists
no archaeological, historic or ethnohistoric data to suggest
that any such mass sacrifices -- numbering in the thousands,
or even hundreds -- took place in the Maya world."
Then there was this college Prof who, to his chagrin, made his class see the movie; here's a clip from the article:
He took issue with the fact that, in his mind, the movie
presents an overly simplified situation that sets up civilization
as evil and unfettered life in the jungle as pure.
"But you learned from this that civilization is bad, and all that
learning stuff is bad, so I hope that you've learned from this
to wander off from Vanderbilt, not even finish your exams and
go off into the woods and hunt pigs sadistically," he told his students.
But again, there is no reason to expect the Gibson's to be true to facts because that's not what they care about. Furthermore, their grasp of just what "history" is as a discipline is a bit shaky:
"There's always this conceit among historians, particularly
European historians, that history only began when they
arrived - which of course is not the case," he said.
"I thought it would be interesting to tell a story that wasn't
from the New World point of view."
All I would say to Mel is that the word "prehistoric" is in our language for a reason; that's why we have archeologists and anthropologists to tell us about the stuff that was not written down by conceited Europeans.
http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2006/12/11/DDG5KMSDK51.DTL&hw=Gibson&sn=001&sc=1000
http://ww4report.com/node/2898/
http://www.canada.com/montrealgazette/news/arts/story.html?id=5dd815af-5b8d-45f1-b261-df828ce3b880