Neither movie attempts to be unbiased, but here is one fascinating aspect. Both men relate passionately to the suffering of the Holocaust and each places the primary blame on the other's side. So, Maher says it was a religious atrocity, or at least that Christians fostered antisemitism and religious believers were the ones committing the majority of atrocious acts. Stein says that atheistic Darwinism (giving rise to eugenics) was the underlying and driving theoretical basis of the Holocaust.
Of course, it doesn't have to be an either/or. Christian eugenicists were considered quite "progressive" even in the United States in the early decades of the 20th century. What's interesting is the way their allegiances and goals cause each comic to absolve the "contribution" of his constituents (theists/Darwinists). Interesting and totally "natural."