To some degree, the film sets up two responses to an apocalyptic event: You've got Howard's individualist approach, all about saving yourself...saving Michelle is really an extension of his self-interest; and you've got Michelle's choice at the end, to be part of a communal effort. Like was mentioned, this directly connects to her past failure to look beyond her own comfort (her need to avoid the distress of facing up the abuse her father visited on her) to help the girl in the store. Take it down a few notches, and it seems to be an argument against libertarianism more generally.
I'm a bit conflicted about the ending, though it does effectively secure the above theme. When she escapes the bunker and for a spell seems to think all is clear, it feels like a moment of her finally escaping the mental and physical abuse, of Howard and of her father before that. The whole bunker situation, with its pitch-perfect fluctuations between convincing you of Howard's mendacity and convincing you that what he says is true, is a great example of gaslighting...he's really playing her mind so she can't trust her instincts and her senses, in order to keep her captive. In revealing that his fears were justified, even as his morality was twisted, forecloses this interpretation.
The other issue with an ending that turns in one clear direction is that it is a bit of a Schrodinger's cat situation. It's a lot more interesting when the cat is both alive and dead. Once you open the box, you've just got a living or a dead cat, not both. The bunker is a closed box, the world has both ended and hasn't. It is this uncertainty that makes the film so gripping. With the film deciding to open the box and expose the dead cat, it can't help but become less interesting. The debatable quality of the gap between seeing the dead cat and the thematically rich decision at the end is really the film's only weakness. I just think that could have been handled better, having made the decision to go in that direction.