No, Philip Seymour Hoffman is not a Scientologist. I even went through a long list of famous Scientologists just to make sure.
The reason you might be confused is that, one of the last projects Philip Seymour Hoffman worked on before he passed away is a movie called The Master, which is based on Scientology.
It looks pretty deep, so my kind of movie. I plan to see it if I can find someone to take me ;-)