While Tom Cruise certainly doesn't have the box office power he once did, it's hard to know how much of his decline is due to his affiliation with Scientology. There are other key factors to consider as well, mostly his age, as younger, sexier hunks have taken his place in the hearts of the movie-going public. Instead of transitioning to supporting parts or character roles, Cruise has insisted on remaining the leading man well into his 50's, mostly in action films--doing dangerous stunts, wooing the ladies, and carrying the film.
He doesn't work with high-caliber directors like he once did (Steven Spielberg, Stanley Kubrick, Martin Scorsese), but it's impossible to know if Scientology is the reason for this or something else. It was widely reported at the time that Spielberg was unhappy with the way Cruise conducted himself while doing publicity for their movie, “Minority Report.” While promoting that film, Cruise made his infamous appearance on “Oprah,” jumping on her sofa, and declaring his undying loving for Katie Holmes after dating only a few weeks. Spielberg believed his outrageous antics distracted from the movie, and who can argue with that!
While Cruise may be disappointed that his star has dimmed in Hollywood, he gets more than enough acclaim, attention, and accolades in the Scientology universe. While some members have left the religion because they oppose the ruthlessness of David Miscavige, Cruise has probably stayed because of his close relationship with the church's leader. The two men are reportedly best buddies who spend a lot of time together. In his book, “Going Clear,” Lawrence Wright details the outrageous things Miscavige has ordered Scientology members to do through the decades to keep Cruise happy: cleaning his homes, repairing his motorcycles, running his errands, babysitting his children, and even helping him with his courtships. Believe me, he has it good and I see no reason why he'd want to leave!