As an atheist myself, I also cannot concive Superman as an atheist. As an humanist and a Raoist I can accept. In fact in the cannon of the DC universe God exists, but his role in the reality is unclear. Also if we are talking about the jewist roots of Superman (which are accurate) Bendis is not saying than Superman suddendly is going to becom to judaism and will start to read the Torah and speak hebrew, but to recover the analogies than are in the heart of the Superman legend.