So as I was geeking out after watching Prometheus, I wondered about the opening scene. First I assume it was a salute to 2001, but also the beginning of life on earth. The had all of the meaning mythology and analogy that Prometheus myth has. A god sacrifices himself to create his children etc. The obvious question after that was, if they went through the trouble of creating us, then why attempt to destroy us. David answered the question during film in which he said, "sometimes, in order to create something, you must first destroy..." The answer was generic, and obviously unsatisfying, so I began to think, and came up with 3 possibilities.
1. The Engineers just have a God complex, and feel like its their right, being a species that is possibly millions of years older than us, or thousands, whatever... I feel like this is a cop out. It didn't explain the visceral hate that the last engineer had for the humans in the scene when he killed Weyland. Especially considering that after the ship crash his first instinct was to make sure that there were no survivors, instead of just going to another ship and taking off to complete his mission.
2. If Ridley Scott doesn't mind the crossover created by the AVP series in the comics and film franchise then another possibility is that they engineered the Predators as well and didn't like the result. They may waged a war against the Predators and not faired so well. Instead of risking another event like that with humans, they opted for a first strike. Its less of a cop out, but doesn't really stick with the themes of the film, I could be wrong.
3. I like this one the most. The Engineers reaction to seeing humans was akin to a vampire hunter's view on Vampires. It had a strong tinge of religious zeal. He attacked without mercy or hesitation. This is purely conjecture, but what if in the Engineers world view so religious prophet foretold of the the destruction of their world at the hands of humans. IT sort of lines up with the fact that Shaw and David are paying them a visit in a ship full of plague. The whole story is a Frankenstein analogy, but it would be poetic if Shaw destroyed them with their own weapon.
Anyway, I guess we'll see. I really enjoyed the movie