Well I figure the film is about 'god's silence' and why that isn't a negative. That's a simplified version of things, but all the same the more I think about the film the more I find that it just coddles to religion. It's better than the work of a fanatic, but as an argument for god let alone one I'm supposed to respect I find it lacking.
I don't think it "coddles" to religion exactly, mainly because it doesn't seem clear that people know what religion it's supposedly supporting. I think many use the information that Malick is a Christian church-goer and I think it's a bit of a red herring. If the film has any ideology spiritually, it's probably Buddhism.
A teacher, like say , Alan Watts, always talked about being in the moment. That's what yoga, for instance, is about. It's not that it's good for you, it's that it's the one activity you do for the sake of it; something you do without any intended result. That, and a tenant of Buddhism is that everyone is one with the universe and all that has life, and any sense of individualism is an assertion of the ego (which is why the universe creation stuff and the dinosaur stuff isn't out of place; the point is that everything is essentially the same story
. The story of the raptor is the story of the boy, etc., etc.). Incidentally, The New World is also Buddhist in some ways, particularly in it's ending. It doesn't view death as the end, but merely apart of the process of life, which is continuous and everlasting (hence water flowing, ships heading to sea, wind blowing in the trees inter-cut with her dying).
The film is fairly obviously (in the sense that it's stated) about the conflict between nature and grace, and I think Jack's journey is that he goes from someone completely disillusioned and overwhelmed by the world, to someone that sees beauty in the moment itself, and no longer feels engulfed by or separated from it. "God" is in everything, it's not separate from you (again, Buddhist concept). I don't see how this "coddles" to any sort of religion exactly (except Buddhism, if you consider it a religion in the western since). And this is not to say that what the film is "saying" is so incredibly deep or complex or something. I'm not sure how much intellectual complexity matters in poetry. I'm not an expert, but is Whitman's Leaves Of Grass praised for it's thematic depth? What strikes me about it is it's deep feeling and it's conveying of the beauty of the soul and the world (and, of course, America ) and it did so in a way that nobody had done before (and was controversial for it, I might add). I think that's enough.