Oh yeah, it took me a while to remind myself that I was an atheist, a humanist even, instead of a maltheist. I've poured all those feelings into comics just so they wouldn't rot away my own core and turn me against my fellow man.
And even then, because of the part of me whose favorite books are God Bless You Mr. Rosewater and The Brothers Karamazov, the same part that gets rubbed the wrong way by Ditko's Vic, I'm always making sure I'm not writing strawmen, always trying to turn my villains into anti-villains.