I don't think Joplin had the eradication of religion in mind. Rather it was the dogmatic, superstitious aspect of it that he hated. For him, the ultimate message of religion should be along the lines of "be nice and fair to other folks and most of them will be nice and fair to you in return." Shouting scripture while condemning ragtime and doing their best to keep it from their communities was just inexplicable to someone like Joplin who lived and loved his music and just wanted to spread it around for other people to enjoy. He never held a job that wasn't related to playing and/or writing music. It was what he was and what he did and he obviously resented being called immoral for it.

But it's fairly clear that Joplin was not going to waste his time flirting with religion. He had no use for it and no use for religious fanatics attacking him. But I think as long as a religious community had the idea of education being the key to success, Joplin would have no quarrel with them. IOW, I don't think he was anti-religion in the sense of challenging their doctrines. He showed no indications that he cared in the slightest what they believed just so long as they behaved themselves.