The point of the film like it says in the description, do you in her position and take your chances living with the killer who wants to pretend your his daughter or take your chance on the outside with aliens trying to kill you.
I've said something similar in other threads, but when you consider Michelle's point of view the likelihood of an actual attack (aliens, chemical, or otherwise) are teeny tiny. The odds that Howard is unstable and dangerous, well, they aren't even odds. He is dangerous and unstable. I think that the odds of Michelle surviving in that bunker were not so great.
The only reason that I wasn't 100% rooting for Michelle to get out was that the movie's title tips you off as to the ending. So even though I was worried about what would happen when/if she got out, I was always 100% understanding of her desire to escape.