Thank-you everyone for your input, you've given me a lot to think about! I like the idea that David infected Charlie and wanted to preserve the alien fetus for extra insurance for Weyland's immortality, but I like the idea of him doing it to create biological weapons even more. It just makes a lot of sense that way, because as dopelganger mentioned, Weyland Industries is a weapons company. I also like that idea because it shows just how greedy and evil Weyland is. He is on death's door, but is still preoccupied with turning a profit. It can create some good plot points between Elizabeth and David, in what I hope is the inevitable sequal!
@Mr.White: good point, I too completely forgot about that! Charlie basically unknowingly gave David his permission to infect him.
A few of you have mentioned in this thread that David was slowly turning evil and/or starting to rebel. This is something that I disagree with. I believe that David was innately good, and was trying to better understand humanity (as shown in his fascination with Elizabeth and her dreams, and his appreciation for the film to the point that he even dyed his hair to match the main character). Even when the crew was insulting him for being a robot, he never really retaliated. The only times he delivered morally questionable words or actions, was when he was following Weyland's orders - something he really had no control over. He even went out of his way to comfort Elizabeth after her surgery. As goddessonne mentioned, David may have even started to develop feelings for Elizabeth.
@kc2015: I don't believe that David wanted to kill the crew and Weyland. I think that line was delivered because Meredith, on some level, wanted her father out of the way. This colours David's view of a typical family, and when he delivers this line to Elizabeth and she disagrees, he sees what a better person is like. I also think that David acted the way he did in the Engineer ship (activating the holograms, opening the door) because he was again acting under the orders of Weyland. He was doing everything in his power to learn about the Engineers and what they could offer Weyland. I don't think it was a matter of him believing his ideas were better than the humans'. This also explains why Meredith ordered the doctors not to engage the Engineers; she wanted her father out of the way. It's interesting how towards the end of the film, when Weyland suits-up to meet the Engineers, Meredith's humanity comes to surface, and she warns her father that if he continues, he will die.
@Caffeinated Anonymous: The way that I interpreted the scene when Elizabeth discovers Weyland, is that David and the others did not attack her, because they felt there was no need to. By that point, I assumed that they already knew she had the operation via the Prometheus's internal sensors/surveillance. They assumed the alien died because it went through the decontamination process (even on screen, after it was decontaminated, it stopped moving). Because it was already out of the way, there was no need to restrain Elizabeth, and David's more human programming kicked in.
It makes perfect sense now why the operating table was only programmed for males, thank-you for the clarification everyone! The table belonged to Weyland, who had a good chance of needing it in his weakened state. This is further shown when Elizabeth first sees the table. Notice how quickly Meredith snapped at her, telling her not to touch it? She didn't want Elizabeth to learn that it was only for males, possibly leading her to find that Weyland was alive and on board.