People expected a Sci-fi with mindless action instead they got a movie full of mystic and religious symbolism presented in a subtle, really Kubrick kind of way. It's easy to see why so many people got disappointed. But I've no doubt Prometheus will be a cult classic in the future.
@Dule90 I'm sure you'll have your own interpretation about things but I think it's worth reading some of what Ridley Scott himself had to say about it. Be. Do your research afterwards if you feel the movie left you with an empty feeling, i guarantee you it's rewarding.