I strongly believe that a therapist should not be judgmental or question their clients' beliefs, likes, or personality. In fact, a therapist who judges their client shouldn't be a therapist. (There was a recent article in a major newspaper in my country, about a therapist who had basically told a female client that she would never be able to have a happy and fulfilled life unless she had children, since that's the Meaning of Life. That therapist should not be allowed to practice psychotherapy, in my opinion.) I've seen three different therapists; the first two were not particularly well suited for me, but none of them judged me, made fun of me, or expressed any kind of negative opinion about me or my hobbies or anything like that.

A therapist who questions your lack of religious belief sounds particularly dodgy. I think (and hope!) that you're very likely to find a much less judgmental therapist, but it might be a good idea to bring all this up with your psychiatrist before you see the therapist.