I've watched the film twice (still have it via Netflix), and I plan on watching it a third time. It's a good solid science fiction film, w/ exponentially more depth than most blockbusters combined. It *is* confusing, and intentionally so, because the characters themselves are confused about what's happening to them. There is a good amount of psychological subtext going on, and I love the metaphor connecting paint primer w/ trying to fix the past. Absolutely beautiful.
If it's true he's a Christian (and a Christian science fiction writer too!), awesome. The best witness is excellence, and a movie like Primer would do more to get the lapsed and jaded blue staters to think about religion and Christianity positively (once they know the director is a person of faith), than any # of simplistic Left Behind books or Christian bands who rewrite Green Day songs w/ Jesus in the chorus. Creativity counts, God gave us the imagination, let's use it. Carruth has real talent for storytelling, and I look forward to his next film, and I'll pray for his success. You could tell by the director's commentary on the DVD, that he was a family guy who loved his (still married) parents and his siblings.
How do you like NetFlix?
Many theories and other speculation can be read here:
http://www.imdb.com/title/tt0390384/board/nest/18735491