They said it was a content use issue. Its more to do with the use of Star Trek themes and reruns than if there is a god or not. Its a talking cartoon dog people hardly a point to rally around if you think your beliefs are under attack.
The A story here is hilarious, with the whole cast of Star Trek (TNG) acting like a bunch of whiny children, but I think the B story is much more interesting. Brian admits to being an atheist and is shunned by the town. I'm not sure I've seen this topic explored this thoroughly on TV before.