Can't see the youtube at work, but the website is pretty stupid. David's motivations are to get Weyland to the "creators" to keep him alive indefinitely. Why does David poison Holloway? For science, same as in Alien, you know, where the android tried to preserve the alien and let everyone die in the process?
David was also the first to remove his helmet and 'test' the air, now of course there could be consequences, but if you're willing to suspend belief that there is an organism that can evolve extremely rapidly, but can't accept there was no bacterial infections that would kill everyone, you're stupid.
Vickers was a bitch because her father (who she knew was alive) was wasting all these resources to find some fountain of youth, rather than just dying and giving her everything she was entitled to. She didn't believe this alien nonsense, or even care about it. She wanted her money. Now, why she came along might be a more interesting question.
The pilot (and his crew) were going to go "down with the ship" and based on assumptions using scans and some knowledge (the scientists being killed by that goop) that this was a military facility and the ship was header for Earth, he destroyed it.
I think most of you didn't actually watch the fucking movie. And, guess what? Every movie with and kind of plot has holes in it. Fucking deal with it.