He's allegedly gay. (One has to use the word "alleged" when talking about Cruise or Scientology, or they sue you up the wazoo.

) According to Leah Remini and other sources who were Scientologists, one cannot be gay period. Homosexuality doesn't exist in Scientology. There is no such thing to them. There also aren't any mental illnesses, like autism, or whatever John Travolta's son had and died from. (Notice we haven't heard too much from them in regards to Scientology since their son died. And Kelly Preston did admit in public that their son had autism.

It must be heartbreaking knowing he died from not having the proper treatment at the time, and it was due to their beliefs in that "religion."

)
So if one has gay feelings or drives, they must get them documented during one of the MANY Scientology courses. Write it all down & get it verified, (so they have this all in Tom Cruise's own handwriting and witnessed,) and them they purge it out of him with vitamins & supplements.
If Cruise is allegedly gay and can't "get over it" with those vitamins & supplements, then the fault is HIS. If he admits to still having those feelings/drives/compulsions, then he is a shameful failure to Scientology and may be a Suppressive Person himself. Since he has spent so much time with this
cult 
religion which has become a family to him, and has publicly announced over and over how much they have helped him and done for him, he can't have them turn away from him and shun him. And for some reason, he thinks being gay would affect his acting career. He'd lose EVERYTHING, if Scientology or Katie outed him with definitive proof.
There is a GREAT
South Park episode on Tom being in the closet.

It should be on
YouTube. It is one of South Park's most famous & most watched episodes. Scientology can't sue them for
satire.