Kids' movies, as a genre, are the deepest indicator of what we think is acceptable. They are required to be both totally thematically overt (so that kids don't miss the message) and non-controversial (so that parents will like them).
So if you want a good example of what any one director thinks, go watch a Mature Grownup Movie and notice its philosophical assumptions—its worldview. But if you want to see what messages we as a society think are so true that even kids can watch them and not be harmed, go see a kids' movie. Some people think of it as a product of reduction, that kid's movies can't be agenda-laden "message movies" because they have to be so simple; I think it's more that they distill messages into their simplest forms.
Free Birds starts from some overt, maybe troublesome (for parents, anyway) philosophical assumptions, particularly about faith and religion. And what's fascinating about Free Birds is that it is both a seeming critique of religion cribbed straight from existentialism, and at the same time a deeply American movie. It's an unusual combination, and a potentially worrying one to see in a children's movie.
Free Birds tells the story of Reggie (Owen Wilson), a turkey at a free-range turkey farm somewhere in the unidentified but corn-opulent midwest. He stands out from his fellow turkeys in that he is smart, whereas they are very not.
Reggie's the only turkey who realizes they're being fattened up for the Thanksgiving slaughter, but when he tries to warn his clan, they turn on him and "sacrifice him" to the farmers—who turn out to be the family visited by the President of the United States, selecting a turkey to pardon. Reggie is pardoned and brought back to live with the president, until a commando-like turkey named Jake (Woody Harrelson) abducts him. Jake hopes to take Reggie back into the past to the first Thanksgiving and prevent turkey from becoming the primary ingredient of a delicious Thanksgiving.
You can already see the weird religious parallels starting to emerge: the stupid and ignorant turkeys at Reggie's home, as they're being carried off to be decapitated by the farmer, imagine that they're going to "Turkey Paradise," and celebrate the farmers as being kind and all-powerful rulers. Reggie's flock is exclusive and stupid and collectivist and refuses to listen to the "reason" of people better than them, and, it is strongly implied, represent your average Midwestern Americans.
The Indian turkeys of 1621, in contrast, don't have any notable religious beliefs. But they look at death with an almost eastern mysticism-like transience. The death of an elder is commemorated by a circular air current of feathers that rises up out of their roost and blows away in the wind, here one day and gone the next. In most respects, the Indian turkeys are smarter and happier than modern-day American turkeys, and so it's hard to see that point as anything but an endorsement of at least a-religious sentiment.