It's possible to be prejudiced against someone based on the choices in life they make. Roddenberry's attitude towards religion was blatantly prejudicial.
As per Braga: "In Gene Roddenberry's imagining of the future [...] religion is completely gone. Not a single human being on Earth believes in any of the nonsense that has plagued our civilization for thousands of years. This was an important part of Roddenberry's mythology. He, himself, was a secular humanist and made it well-known to writers of Star Trek and Star Trek: The Next Generation that religion and superstition and mystical thinking were not to be part of his universe. On Roddenberry's future Earth, everyone is an atheist. And that world is the better for it."
That kind of thinking is prejudicial.
Religion is not a "plague." Religion is not all "nonsense," "superstition" or "mystical thinking" and getting rid of it will not automatically make the world a better place. That's the kind of person who believes that all people of faith are evil backwards people, and that is prejudice.