I'm surprised by this as well. It was a completely competent film, and I was relatively engaged while watching it on initial viewing, but I didn't think it would hold peoples affections to strongly months after it's release.
I appreciate that it integrates a faux-documentary style with a classic cinematic structure without being too clumsy, makes fine use of special effects, and delivers a terrific performance by an unknown actor (and to do all this within a relatively large summer film as well)... but that doesn't make it any more interesting on repeat viewings. At this point, seeing it again would almost be a chore.
Really, every film nominated in this category was superior to District 9.
I also don't understand the comparisons to Children of Men, other than they belong in the same section at the video store.