Listen to Dahlia Lithwick discuss this topic on NPR's Day to Day.
That seems unfair to religious citizens who seek some sort of "balance" in the law—equality for religious and atheist alike; equality for majority and minority religions. But what does "equality" mean when you're talking about religion and particularly state-sponsored religion? Doesn't it mean that some religions will necessarily be more equal than others? The framers seemed to think that was an appalling prospect for religious freedom.
One of the hard lessons of the religion cases is that if the public square is going to welcome everyone, it cannot necessarily welcome all of their gods. Perhaps the most American sentiment of all is the faith that somehow, He will be there anyhow.