The following is a spoiler of the final scenes of Prometheus :
Why did the engineer bother to try and kill Dr. Shaw after the ships were damaged?
In the scene where the Engineer wakes up on the wrong side of the bed, Dr. Shaw starts running to escape. After he has caused damage to those in the immediate vicinity, and while fully aware that Dr. Shaw is escaping, he turns to the controls and initiates a lift-off.
OK. That makes some sense, he already knows there is an infestation in the complex. She might well be killed during the take-off, or by the infestation, and if not, she is of little consequence, since she is returning to the ship controlled (supposedly) by the old guy that politely asked the Engineer to save him. So the ship is presumably not a military ship.
Little does he know that the pilot is determined or insane enough to ram his ship!
Once grounded, he could have run to another ship (now confident of no air traffic congestion) and escaped in it. It would probably have also been loaded with cargo, so he could continue the job he was meant to do, but instead, he ..goes running after Dr. Shaw.
He might have presumed she had time to get to back to Weylan's ship, set it to collide with his & escape in the life-pod, so he has every reason to be upset with her, but what is the point beyond petty revenge?
I'm not even going to suggest that the entire reason he did so was so that we could see his end fate, and the result of that. No, that would just be too tacky.