I believe he is highlighting how Scientology is more of a grift than an actual religion. I would be more concerned, all else equal, if a Scientologist was President than if said President was American Protestant or Catholic.
edit: It could also have to do with Scientology’s history of child sex abuse
Scientology isn't a religion it's a cult/grift. For decades they were denied the tax status of a religious organization because they didn't meet the legal test until they mounted a decade long infiltration and harassment campaign to which the IRS eventually relented.
edit: It could also have to do with Scientology’s history of child sex abuse