Coming on close to a year since the movie came out - a question struck me -- what if the Engineers had no plans to exterminate humanity out of any malice or the need to correct a possible "mistake", but rather the Last Engineer's (aborted) mission was really just an extension of a plan to exterminate themselves?
It's heavily implied in the film (and pretty much taken for granted I think) that the Engineers are the progenitors/creators of humanity via seeding Earth with DNA that eventually gave rise to human life. Shaw tests the DNA from the head/body found at the entrance of the ampule room, and it gives what we can assume was a species match.
So, what if, the Engineers decided somewhere along the line that they were a problem, that they had to be removed from the universe? If this were the case (and this is purely hypothetical), wouldn't it be logical that if they were to decide to commit a collective suicide/genocide of themselves for whatever reason, then, naturally, they would also by extension necessarily also have to destroy humanity as well?
If they didn't do so, then it would defeat the purpose of them exterminating themselves, as what is essentially the same species would continue in humanity which would have the potential to become whatever it was the Engineers had become.
I'm not necessarily saying I believe this theory to be the case, but a few things struck me as possibly leading some credence to it. Namely, the Last Engineer (we don't however know if he's the last of his race, or the last one left on LV-223), and the cessation of Engineer interaction with humanity at least 1500 years ago.
This is tgbyhn btw, for some reason the Google authentication isn't working for my account. Using the temp account I created last time I had these problems.