I think this is a example of Christian Privilege snuffing out and oppressing the anti-christian voice. Turning this into a white privilege issue is a fallacious race generalization that excludes atheists of color. Also, focusing on white privilege misses another important issue.
If a billboard read, "Millions of people are good without Zeus," people would criticize it for being a waste of money, not offensive. Changing Zeus to God becomes offensive because the Christian Hegemony throughout history, specifically United Sates History, has established as sacred the mention of God in public. The backlash against this atheist advertisement is because the belief in Christianity is seen as a social norm, more so in certain areas of the country where anything against may even be a taboo.
It would be interesting to consider what kind of a reaction would arise from atheist advertisement saying, "Millions of people are good without Allah." I really don't know what would happen. Would it be a stronger reaction? A smaller reaction? More or less critical?