Prometheus is a brilliant, and largely misunderstood, film.
It is the story of an android, David, his anger towards his creators, and his curiosity about their creators. David is the protagonist and humanity is the antagonist.
We are meant to despise the stupid “scientists” just as David does.
A good 70% of the story is told, and carried, by Michael Fassbender’s body language and facial expressions as David. Another 28% is Noomi Rapace’s body language as Elizabeth Shaw. The rest is just scenery and mood. The actual lines of dialogue tell you almost nothing about the characters, their motives, or what is actually going on in the film.