I have no problem with superstitions and individual spiritual experiences (even belief in a supernatural being) will survive for as long as humanity survives. However, I do hope that Roddenberry's vision of no organized religion, with religious figures in positions of authority and religious principles as foundations for secular laws (except in cases where such principles transcend individual religions, as in "You shall not commit murder") will come to pass. In fact, such developments have been underway in the West (at least outside the US) since the mid-20th century if not earlier.
organized religion at its simplest is just groups of like-minded people with similar beliefs coming together. I don't see how it disappears completely without the kind of oppression that wouldn't fit an optimistic future.
But yes, organized religion stripped of its previous power and influence does seem like a reasonable extrapolation, since as you mentioned, that trend's already underway in a lot of places.