Always be suspicious of any criticism that assumes the content of a story is meant as a polemic for the storyteller's views. That demonstrates a misunderstanding of the creative process. Yes, some storytellers use fiction as polemic, but often, writers will welcome the opportunity to explore characters with different beliefs from their own, or fantasy universes that don't reflect their real views, because they think there's an interesting story to tell there. For instance, X-Files creator Chris Carter doesn't really believe in UFOs, psychic powers, and the like; he just thought they were an entertaining subject for a work of fiction. And the beliefs of Firefly's lead character Mal Reynolds are almost diametrically opposite those of his creator Joss Whedon, who's said he probably wouldn't get along well with Mal if they met. But he found Mal an interesting character to write about nonetheless. Also, J. Michael Straczynski is an atheist, but a number of his Babylon 5 characters had sincere religious beliefs that were portrayed positively.
So it's naive to assume that if a storyteller includes spirituality in a work of fiction, it's meant as proselytization for that storyteller's own religious views. Often it's just because the storyteller thinks there's something creatively interesting there. In the case of Galactica, I think it was just part of Moore's desire to make the show into the anti-Star Trek; ST took a relentlessly secular view of the world, and so he wanted to do something that was different when he got his own show (and he and his colleagues on Deep Space Nine certainly pushed for more spirituality there as well). It's also worth keeping in mind that Moore's BSG was a remake of a concept that had been intended by its creator Glen A. Larson as a space-opera retelling of the Book of Mormon, and which was heavily steeped in the ancient-astronaut lore that was popular at the time. A degree of mysticism and spirituality was intrinsic to the premise of BSG, so it could be argued that Moore was just being true to that.
And Locutus is right -- spirituality is not the same thing as religion. Exploring questions about the nature of existence, the possibility of an afterlife, etc. is not the same as advocating a particular organized faith and its ideology.
Of course, it could be argued that neither BSG nor Lost was really science fiction in the final analysis. I think they both fell more into the genre called "magic realism," i.e. fantasy set in a familiar, grounded world rather than a medieval sword-and-sorcery type of setting, although BSG was a novel hybrid of magic realism and space opera. Still, there's plenty of overlap among the subgenres of speculative fiction, and it's not necessarily a good idea to draw sharp dividing lines between them, especially in mass-media entertainment, where you want to have broad rather than niche appeal.
Now, personally, I've felt for a long time that there's too much fantasy and mysticism in genre TV for my tastes. I would like to see more hard-science shows. But the predominance of fantasy was a fact of life long before Lost or Moore's BSG was even a glimmer in a producer's eye. Heck, go back to the '80s and you've got Quantum Leap all but saying that God was behind Sam's journeys. Plus you've got the outright fantasies of the '90s like Hercules/Xena and Buffy/Angel. So it can hardly be said to be a new trend.
