All this about Engineers seeding life on earth, guiding ancient cultures then disappearing clearly suggests that humans aren't some kind of experiment. Why wait for us to fly to them when they could have rounded up a couple tribes, dropped them into cryo sleep then done the experimentation in a nice sterile environment?
The question the movie is asking is why are we here. I think the movie is saying we were created for worship, to worship the engineers as gods. We cast them down, sought to usurp their power and make it our own and therefor we had to be destroyed. Hence Prometheus: the man that stole fire from the gods, only to be punished in a really shit way for all eternity.
The dead engineer who's head exploded was carbon dated to 2000 years, the birth of Jesus, the "end" of the pagan gods. So when Jesus was born, this weapons facility was in the process of deploying a WMD to Earth when the Engineers themselves were caught playing with fire (there may be more here: We created David, We were created by the engineers... who were they created by and was their own demise a "Prometheus" story?) and got burned, their WMD got loose and killed them. Perhaps the black oil substance was their own fire, stolen from their gods.
As far as I see it that fits with the vague assertions of the writer/director and has enough pseudo-philosophical oomph to be considered "deep" and "thought provoking".
Of course I could be wrong.
[edit] Missed some of the talk of "killing the parents" if you will, think it only reinforces the above point. David, in the early part of the film, is seen doing "human stuff": Watching movies, shooting hoops. He's obviously not human, he's not doing those human activities right. He *has* to be human and he resents us for it, for making him the way he is. He feels cheated that he is obviously superior to his creators and yet bound by their wants and needs (has to wear the helmet to keep up appearances, follow the directives of his father despite not agreeing with them). He attempts his own coup from his literal and figurative creator, and gets his head torn off for all his trouble. At the end of the film, both he and Dr. Shaw demonstrate a kind of mutual respect for one another, both having been "humbled" trying to steal fire from the gods.
Now I'm starting in on the pseudo-intellectual bullcrap...