I hate to say it but there's so much potential there. You even see the original ending there, ready made for the movie. However, pow, God did it. Really, had the reasoning for the survivalist colony been "I heard on the radio from somewhere else" or "I have actual information from the mainland and you've been cut off from everything for years" sure. It was attributed to God. And I daresay 90% of the world population dropping dead, 9% going zombie, and 1% surviving to be eaten by the zombies is a good argument for the non-existence of an all-powerful benevolent god. Certainly, atheism is called for, but a mountain town... not really.
Also, if you have three years and know exactly what you're fighting. You might want to have a better defended base of operations.
The original ending to the film was that he was the monster. The people were still alive and kind of messed up, but he was the monster going about and killing them. He kidnapped a woman. The same man who tried to save her by running a bit out in the sun was the same who set the trap with the manikin, and who lead the attack on his house at the end. Really, he was trying to save the woman the doctor took. He was just going around murdering people willy-nilly... and it was really he who was the monster. Zing. That would have been the right ending, and a good one at that... but no... atheist doctor can't even believe in a mountain town. If you can't believe in God you can't believe in anything. Also, a number of his defenses were actually good enough. You're telling me a vault in the basement isn't enough? And what the hell good were those lights? He used them a lot for being completely ineffective.
It was 98% of a great movie. I hope they offer alternate endings on the DVD.