I'm not sure that I agree at all.
Joss Whedon is an atheist himself and although he does not push The Atheist Cause™ in any of his shows, the fact that the one religious man in Firefly is portrayed as one of the good guys isn't really to my mind an indication that religion was being given a hat-tip. The hero Mal is quite overtly an atheist (and an angry one at that) and the troubled wunderkind of the series, River, is an atheist too. Remember the episode where she tears Shepherd Book's bible up for being wrong? Also, Book's history seems to be a possibly shady and malevolent one. On more than one occasion there are hints that his turning to religion was a result of trauma from his previous career.
The no aliens in space thing was in my understanding nothing whatsoever to do with God only creating life on earth. It's one of the possibly less benign after-effects of Star Trek that there is a general assumption that Sci-Fi must mean has talking aliens in. It was a brave move to try to do Sci-Fi that broke away from this slightly unlikely idea that the galaxy is populated by other humanoid species to the entirely plausible idea that we might well be the only space-faring species out there at this particular time.
I'd love to discuss this in more detail if you'd like.
Wow that's a rebuttal! and I don't mean that in a mean sarcastic way, as I had no idea that Whedon was an atheist and I had forgotten/overlooked the part of Shepard's past.
I remember reading something in the Star Trek Encyclopaedia on an episode (not sure what series) where it was discovered that an ancient alien civilization seeded a load of planets, thus explaining all the humanoid species in the universe. It was merely a way of glossing over the fallacy of the Star Trek universe containing mainly humanoid species. Ironically, this in essence was introducing the idea of intelligent design, even though the original creator Roddenberry was an atheist! But I suppose they didn't have a choice, the bed had been made with the original series and nobody really questioned the whole humanoid species in the galaxy when Star Trek was first created, so it's hard to fault them on that one. To be fair they did introduce Species 8472 in Voyager, which as a far as I remember were not humanoid, but took on humanoid forms in order to communicate with Janeway and the crew, never really liked Voyager though, it tired Star Trek some bit, and Enterprise just pulled the plug on it. Still, to the best of my knowledge the franchise has never supported the idea of a benevolent god that created the universe and/or life.
Going back to Firefly, I suppose I always just get a bit paranoid with anything FOX produces, a lot of this has to do with I doing a module on Deconstruction while I was doing literature in college, I just analyse everything to the max! Look at the Simpson's (FOX again) some people say it's a bad example to children, and yes it can be if you are picky, but it is also pretty conservative when you begin to deconstruct it. That's how I analysed Firefly, preacher on board, no aliens, and the overriding factor of FOX!. I also assumed Whedon to be a believer, especially with his involvement in Buffy, where the supernatural was the central theme. Looking at it now, I was jumping to conclusions...