Like most successful people Gene Roddenberry is starting to drink his own Kool-Aid. Imagine if everything you touched turned to gold, you would begin to think that everyone worshipped you too. He may have made the statement that he "could have created a religion" in an off the cuff way but he obviously took the time to think about it.
Gene Roddenberry gained a massive following by creating the series "Star Trek". The idea that he could have created a religion as well was maybe said in jest but is actually a true sentiment. The series impacted millions, and featured groundbreaking moments, such as the first interracial kiss on television. The series had intensely dedicated fans, and if Roddenberry wanted to create a religious framework around it, he would have had followers.
Gene Roddenberry knew that Scientology was created by Ron Hubbard, rather than discovered by him. They were close friends at one point, and he knew that Hubbard used his talents of writing stories and his imagination to create a somewhat believable myth about the way the univese works and decided to call him on it.
Decades of shows, millions of fans Gene Roddenberry could easily have established a religion and had an instant following of Trekkies. The common core principals in all the movies and shows would have made a decent foundation that many would have found easy to follow. Perhaps even improving upon lives of others and not interfering should have been a goal of humanity in all regions of the globe.