Personally I find it is fantastic and intricately plotted and woven film and all that. It somehow managed to exceed my expectations. I've seen it multiple times and am still pretty obsessed with it. I'm confident that it will go on that short list of movies I can watch over and over again.
I get that some people just don't like Prometheus, taste in film varies for everyone, but am surprised at some of the outright contempt toward it. So I have been trying to wrap my head around why that is beyond the whole "the scientists act too stupid" type of surface criticism as why somebody wouldn't like it or connect with it.
So these aren't meant as criticism from my perspective, I wouldn't change anything about it (except for maybe a longer cut), just possible reasons why many people didn't connect with the film:
1. The majority of characters are not overly likeable in a classic sense. Shaw as a lead is difficult to identify with; she starts out her journey as a naive religious fanatic. David, the awesome robot is a huge a-hole. Even Janek at times has somewhat of a dickish edge to him. I could go on down the list but you get the idea. I'm not suggesting anyone doesn't like the characters (I do), just that they are not immediately likeable in a Brett/Hicks/Ripley way.
2. There's no real triumph in the film. Aside from the brief crash sequence, which comes as no surprise to the viewer as its in every trailer and poster, no great fight feels won. (partially perhaps its because we know Earth is never in peril as it's still there in Alien.) I feel the payoffs are there to the story but it's very bleak - along the lines of the Alien 3 sense of bleak, and that film wasn't well liked.
3. Shaw's storyline is a horrific nightmare. She starts out with extremely high and positive expectations, and then is subjected to the most horrendous sequence of betrayals, events, cruel irony, certain death, and so on. It's as if the whole film exists merely to sadistically torture this character. Shaw never gets to earn respect from any of the other characters. Aside from brief moments at the end, she never gets to "take control" of the situation in a Ripley like fashion.
4. The lack of horror. The trailers (and Ridley himself) promise that it will be scary. It's not overly scary in a classic sense. It's tense. There are certainly memorable moments of body horror that live up to the franchise, but the overall horror is more existential philosophical musings, not physical screen terror.