As bad as Scientology is, it has a strong libertarian anti-government streak, and has from the beginning. L. Ron Hubbard was crazy and evil, but he was right about some things. In the 1940s, he even wrote a pulp story in which he critiqued a bad FDR policy (destroying food in order to keep food prices up). He infused Scientology with a lot of views like distrust of the pharmaceutical industry, distrust of government, distrust of psychiatry, etc, that push quite a few Scientologists toward the right politically.

Kirstie Alley was both a Scientologist and an open Trump supporter. In 2020, Trish Duggan (a wealthy Scientologist) donated $4 million to a pro-Trump super PAC.

There's even a Scientologist who wrote a book claiming that Trump rescued Scientology from the Deep State (frankly I'd take anything he says with a massive grain of salt, though):

https://www.amazon.com/Trump-Rescued-Scientology-Deep-State/dp/3947982100

Tom Cruise and John Travolta both stay out of politics publicly, although I've read that Travolta may have hobnobbed with the Clintons a bit behind the scenes (to be fair, Trump was on friendly terms with them at one time too).

Cruise in particular is an enigma. The impression I get of him is that he's well-meaning but hopelessly brainwashed, and also has a massive ego brought about by Scientology's leadership filling his head with ideas that he's some sort of world savior. Multiple ex-Scientologist whistleblowers say that Cruise used to be a down-to-earth person decades ago, but is now very controlling and demanding toward lower-ranking members. Supposedly he threw one against a refrigerator for some minor offense (not cleaning a room well enough, if I recall right). On the other hand, they say Travolta is a complete "Teddy bear", very sweet and nice to everyone.

As a movie producer (he produces most of the movies he stars in and has full creative control), Cruise is one of the few in Hollywood today whose movies tend to be wholesome in their messaging, without leftist politics or other insidious themes. His latest Mission: Impossible movie is even full of Christian salvation themes for some reason, which is odd considering that he isn't Christian.

Scientology seems to be competition for the Deep State. Decades ago, Scientology conducted a large-scale infiltration of the IRS and used it to blackmail the U.S. Government into giving Scientology official status as a religion and tax-exempt status. The impression I get is that the Deep State didn't like this (it was essentially their own game being used against them).

Whistleblowers (such as Leah Remini) exposing the evils of Scientology have been given free rein and a large platform to do so by Deep State-controlled mainstream media outlets. These same media outlets have been openly critical of Scientology for decades (remember how negatively Tom Cruise was depicted in the media after his Oprah couch-jumping incident, for example).

This isn't to say that Scientology is good (it's very much a cult) or that it poses an existential threat to the Deep State the way Trump does, but I think that the Deep State sees Scientology as unsanctioned competition and a nuisance that needs to go away.