Just saw it last night and really enjoyed it. It wasn't until the flood part that I got the biblical parallels, but that definitely made it more enjoyable to follow it going forward (as in, it's not as surprising when the baby dies).
I can definitely understand why it's not for everyone, but a pretty awesome theatrical experience, and definitely unlike most anything else seen before. And props to the director for pulling off an allegory as a wide-release, feature-length movie.
I think stylizing the early parts as a potential horror movie make it especially effective. God has created this beautiful place, and she watches it get destroyed by his followers. You might not agree with the environmental or social perspective, but he does a pretty cool job pulling this off.
Also, I read the Aronofsky's main message was environmental first, and that the biblical parallel's were just there to function as a solid story structure, because that's the predominant view of the history of mankind by westerners.