I never understood why science-fiction films take a crap on religion or just ignore religion entirely which is even less realistic. There's going to be conflict on creation vs. evolution. There's going to be evolution on "God did it" vs. "science did it, but we don't know how." Beyond these two conflicts, what's the problem?
Take Star Trek as an easy example. I understand Gene Roddenberry's idea of religion more or less being gone by the time mankind spreads across the stars via their starships. However, there's a big difference between "faith" and "religion." Why can't "some" of the crew be religious? Imagine you have an episode where say 5 characters are trapped in an isolated part of the ship where the hull is going to breach, and no one can get to them in time. One character prays, say the other 4 are atheists and are just trying to "make peace" with dying. Just in the nick of time, everyone is rescued at the very last second because science. At the end of the episode, there could be discussion about "divine intervention" vs. science. There could also be discussion on whether X character's religion is "real" or just "brings him peace and comfort." Given that Star Trek is more philosophical sci-fi, this would fit, would it not?
Star Trek: Deep Space Nine tried to handle this by handling a fictional religion for the Bajorans who look human with wrinkled noses and paler skin. There's this "one" wormhole that's special, because it's the only known wormhole that's stable. Aliens live in the wormhole. To the Bajorans, space gods. To everyone else, ET. It's a nice parallel to the religion/atheist contrast in real life.
I'm not saying sci-fi should be religious. We go to the movies and watch TV for entertainment. For those of us who want a sermon, we read go to Church, watch YouTube, or read a book. That said, I just think it would add some depth to sci-fi for some religious characters just like you see in any other genre.
Though I'm Christian, I tried to leave religion open so everyone can join in.