FYI if you really want to know there's a guy on YouTube (Kroft) that has done dozens of very good videos on the Alien movies. He breaks down what was said as it was in the original script. And it's interesting and would have made a better movie, but I think Scott chickened out of the potential controversy.

Long and short of it is that >!2000 years ago the Engineers had taken a human to their home world and trained him and enlightened him and sent him back to earth to spread the message but his compatriots nailed him to a cross.!<

!The Engineers, therefore, decided that our race was a failed experiment and decided to exterminate us but their own weapons got away from them and killed them before they could pull it off.!<

There's more to it, but go watch Kroft's videos if you want to know more.