There is an important sense in which the discussion about atheism is a struggle for the civil rights of not only atheists, but non-theists in general (agnostics, Unitarians, "apatheists", etc.) as well as non-Christians and minority-sect Christians.
To most atheists, the discrimination and oppression most of us face is blatantly obvious. But even a sensitive, ethically admirable guy such as the Deacon is just now "getting it". So perhaps it's useful to once again present some of the most obvious evidence.
Bush pere stated that atheists should not be considered citizens or patriots. The worst insult that Ann Coulter can offer to liberals is that they are "godless" (cf. "godless Communism"). "In God We Trust" is on our currency and "Under God" is in the Pledge of Allegiance. Joe Lieberman, a "Democrat", asserts that "separation of church and state... promises freedom of religion, not freedom from religion," and (misquoting Washington) rejects "the supposition that morality can be maintained without religion."
And that's just in the public sphere. Freethinking teens, young adults and even middle-aged children in religious families face often face profound oppression. Even questioning the absolute truth of the family's religious belief is frequently grounds for ostracism and for minors at worst imprisonment, torture and even murder.
Throw in Creationism/Intelligent Design and Theocratic Dominionism and it's clear to see there's a problem.
 These statements were the biggest reason I didn't vote for Gore in 2000. The article notes that Lieberman backed away from his remarks, but I find his change of heart insincere.