Charlize is fine in the film, her part isn't the biggest but she handles it very well.
It's just... I was expecting this to be more, I guess. I expected an epic, sweeping movie, something involving. I expected grand revelations about the place they were headed to.
What we get is, basically, a bunch of monsters. And there's no real logic to the monsters, they're just... monsters that do monster things because they are monstrous. It comes across like somebody sat down and said "And what if you chopped a bit off it, and then that bit turned into a different monster! And what if it like drooled on the floor and somebody touched the drool and that made the drool come alive and turn into another type of monster!"
Those are made up examples, by the way. Not spoilers. But that's roughly how it is... the original Xenomorph had a really simple, easy to understand, relatable life cycle and manner of behaving. We saw how it was born, how it grew, we saw it killing, sleeping... we almost got to know it as a character. In Prometheus they seemed to just want a lot of different monsters in there doing gross stuff in hopes that it would look really cool. There's no depth to it.
I believe one of the writers from Lost wrote this, and it shows. I gave up on Lost because it kept endlessly dangling tantalising questions, and hinting that deep things were going on, but then it rapidly became clear that this was all surface show - the writers didn't really have any plan, they just made it up as they went along. That's how Prometheus comes across. A lot of potential issues and questions raised, and then they're just kind of left there. I get the distinct impression that the script wants to be deep and meaningful, but doesn't really know how to be.
Maybe I did expect too much. If you want to see cool stuff on screen and monsters doing their monster thing, you may well enjoy it far more than I did.
Give a man a fire, and you keep him warm for a day. SET a man on fire, and you will keep him warm for the rest of his life...