Originally Posted by
Lutz
Spoiler: It's because the initial set up of the movie with the cave paintings involves the engineers being the interactive (pre christian) gods of society. The Greek/Egyptian gods etc were physical and they interacted with the day to day social workings of people. When humans moved away from the engineers and created secular religion the engineers decided to destroy them.
It also changes the ending of the movie where it isn't actually just a shameless set up for the sequel; it's the folly of the main character failing to realise that it was her own faith that was the reason the engineers wanted to destroy them. It's very similar to the ending of Blade Runner finding the unicorn and then going into the elevator with the doors closing to an open end. Shaw is flying off in sheer arrogance of everything that has happened and her last monologue to David about finding out why the gods decided to destroy humans is also trying to point the audience back to the explanation which is contained within the movie.
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