Certainly one could also harp on the Catholic themes in the novels of Graham Greene and yield a bounty of evidence ; we don't, however , tend to get bent out of shape over the religious overtones of the novels or their more sinister implications and instead prefer to enjoy a good yarn. Greene was good at writing good yarns.
The main concern with Cruise isn't whether his movies have a subtext endorsing a controversial cult, but whether Cruise is consistently adept at choosing good movies to star in. Like anyone else in the public eye and who stars in movies, his track record is uneven, although his batting average is better than Nicholas Cage's. For Cruise himself, he is a puzzling man in terms of his public persona, but my principle concern is if his movies are fully realized entertainments worth the money I work for.
He is not my favorite actor, although I think he's been decent in a couple of things, although I think his best performance, his most legitimately autobiographical (if there is such a thing) was as the quirky hit man in Michael Mann's reasonably sublime. In a grey buzz coat and portraying a sociopath who assumes personalities and points of view whimsically , much the way people change shirts.I suspect Mann had Cruise in mind when he realized he had a character who was all mask and emotional subterfuge. I wonder if Mann's direction of his lead actor included the phrase "just be yourself".