Ahh, that movie. I think at the request of a friend that I just took a whole weekend to sit down and watch the movie, as well as absorb all of it. The great thing about this movie is the fact that you can interpret it in whatever way that you want to. I have had heard people say that it is about time travel, physics, parallel universes and tangent universes, dreaming, and seeing the future.
The best thing to do is go to the movie's website and check it out, they have an actual copy of the fake book, "The Philosophy of Time Travel". It makes more sense of the movie, whether or not the director intened it that way.
The best interpretation that I have read and/or heard is on this website, I recommend you check it out if you liked the movie:
http://www.anthroid.net/autopsiadonniedarko.htm