That would depend on what part of Roddenberry's life you're referring to, it would be more accurate to say Gene Roddenberry was a atheist at times. The smallest amount of research would reveal that Roddenberry wasn't "always" a atheist. On August 6, 1969, Majel Barrett married Gene Roddenberry in Japan, in a traditional Buddhist-Shinto ceremony. At that time, Roddenberry in multiple interviews professed to being a Buddhist. There no indication that Roddenberry was an atheist during the creation, or production run of TOS. I mentioned before that the novelization of ST:TMP included that Vulcans have the ability to perceive a oneness with The All, the universe's creative force, or God. According to Susan Sackett , who was Gene Roddenberry's personal executive assistant for seventeen years, that part of the novelization came from Roddenberry's own belief in "The All" during the late seventies. (Inside Trek: My Secret Life with Star Trek Creator Gene Roddenberry) Roddenbery's belief in atheism would appear to have been during the last years of his life. His atheist influence upon TNG faded after his death. Problem there is that while Star Trek is Gene Roddenberry's original idea, it really never was solely "his show." The idea that assembled into the Star Trek we all know, came with considerable help from others. Roddenberry came up with several story ideas, but (as noted previously) actually wrote very few of the scripts. And really the show was as much Gene Coons creation as Roddenberry's. Without Herb Solow's molding of Roddenberry's early nebulas ideas, the show wouldn't have been able to advanced to the pilot stage. Robert Justman also one of the pioneers producers of the show. So it was never "just" Roddenberry's vision of the future on screen at any point. More accurate would be Chaplains are usually from one organized religion, but routinely hold multi-denominational religious services. And provide spiritual support to people who belong to many different religions, denominations and spiritualities. And what happen to the JemHadar fleet in Sacrifice of Angels? Sisko: "You want to be gods? Then be gods, I need a miracle, Bajor needs a miracle, stop those ships." Okay, let's slide this back somewhat towards the OP shall we? From what we've seen on screen, there are people within the Star Trek universe who seriously believe that prayer can achieve a positive result. Praying to the Christian God like Angela at the end of Balance of Terror. Rhada and the Hindu symbol. Chakotay talking to his ancestors. Bajorians and the Prophets. Vulcans and their gods, shrines, temples and monasteries. For these people, the presence of a Chaplain aboard ship would be of service. There are people in the Star Trek universe with whom we don't know one way or the other what they believe. A Chaplain and a ship's chapel might have no place in their lives, but neither would it be of a detriment to them if both were presence somewhere on the ship.