Truth is a god in the way that gravity or magnetism is a god. He's just a manifested force of nature. He's sapient on some level, sure, which is a neat trick, but we managed to make meat think and we're not extraordinarily special about it either. He didn't invent humans and he didn't spawn the universe the way that Rose would have expected the god of her religion to have done; he has minimal to no interest in the day to day lives of any creature and only intervenes when someone actively wanders into his grip of influence. He's not a Capital-G God. Truth is to matter what fire is to flammable objects. He's a metaphorical (and perhaps even allegorical) chemical reaction.

Ed isn't an atheist because he saw god and cussed him out irl; Ed's an atheist because he doesn't believe that the brute force of Truth qualifies as a god. Quite frankly, I think that's a hell of a lot ballsier and a much more complete understanding of the situation. This perspective insulates him against idolizing the Truth as an ultimate divine force and makes Truth something that can be reasoned around or through, rather than with, which would never have worked.