The most obvious flaw in Maher’s documentary is that it’s one sided. He offers many examples of religion that’s extreme, dishonest, hypocritical, or anti-freedom. It’s an often-funny visual tour of bombs exploding and charlatans peddling faith-based snake-oil. In fact, most believers would agree with many of Maher’s attacks. The problem is his conclusion that flim-flam artists and jihadists represent the totality of religion.
It’s hard to know where to begin in rebutting that. For this post, let me just start with a few obvious points about American history. Most major American social reform movements that improved the status of the disenfranchised or maltreated were fueled by religious faith:

Abolitionism
The civil rights movement
The drive to end child labor
Environmentalism
The creation of public schools
Suffrage and women’s rights
The progressive era move to create a social safety net
Creation of the eight hour day.
In addition, much of our charitable sector arose out of religious impulse. Among the institutions of civil society dedicated to social progress that have religious origins:
YMCA
Salvation Army
The Red Cross
Catholic Charities
Habitat for Humanity
Boy Scouts
Goodwill
Alcoholics Anonymous
What have I left out?