In the webcomic Dead Winter (zombie apocalypse), there isn't an evil militia. Evil individuals, sure, but the military does show up. And they are in opposition to the cops. Naturally, the protagonists get caught in the middle.

And in Falling Skies, our protagonists basically are the rag-tag militia, and they do their level best to blow the aliens up. Most of the military was killed by the aliens, though there are a few soldiers left over.