That simply isn't true tho'. The biggest and most famous franchise of all, Star Wars, is heavily religious, the very first film states it openly. So is the best recent sci-fi series Battlestar Galactica. A main character of Firefly is a preacher.

Even in Star Trek the Vulcans spend an awful lot of time contemplating candles and wearing robes. They may not talk about it on-screen but the producers must have consciously chosen to use monastic/Catholic imagery.