In the opening, an Engineer drinks the black goo and then disintegrates or whatever. What happens after that is left to our imagination.
When Weyland & Co. finally meet an Engineer, the Engineer's immediate reaction is violent hate. It's pretty clear -- and this in the text, not subtext -- that the so-called Engineers see humanity as filth, an abomination. It ties in with the myth, that humans needed to be ruled and governed. Or destroyed.
I thought it pretty obvious that the Engineers started life on earth. You see him break up and some new DNA is created from his break up. But if the Engineers thought humanity needed to be governed, destroyed or ruled they could have done it already.
The Engineer who drank the black goo and started life on earth was a rogue. A rebel.
He was Prometheus, giving the gift of "fire." The Engineers left the planet before seeing the results of his actions.
When the Engineer on LV-223 encounters Weyland, it realizes what Prometheus' act had created and its reaction is "
Fuuuuuuuuuuuuuuuuuuuuuck thiiiiiiiiiiiiiiiiiiiiiiis." And so it kills Weyland, decapitates David, and sets out to destroy everything human it can find.
And why does this happen? Hubris. Hubris on Shaw's part, thinking that the cave markings were an "invitation," and hubris on Weyland's part, thinking that he was going to be granted immortality.
And in the end, it all ties into the theme of the film, that some things are better left alone. Even the Engineers realized that the black goo was more powerful than they gave it credit for and they didn't know the true scope of its characteristics.
Edit: And this is why Ridley Scott is an absolute master craftsman. He's brilliant at giving you tiny hints and then telling you, "You figure it out." He doesn't spoon-feed the audience every single minute detail, but rather gives tiny hints along the way, and this is largely due to his background as an art director prior to moving into film direction. This discussion reminds me of people who nit-pick Khan never taking off his other glove in
The Wrath of Khan -- why do
you think he didn't take off the other glove?