A reader at iSteve's thinks that many atheists accept HBD. The logic seems to be that atheists are clear-thinking, tough-minded people who see through sentimental views.
A large sample (6,613) of whites were asked by the GSS about their belief in God, and about whether or not they believe that blacks are innately less intelligent than whites. 4.6 percent of atheists answered yes; 13.6 percent of those who "know God exists" said they believe in innate racial differences.
This pattern is consistent with the view that atheism encourages liberalism, not realism.