You have a freedom OF religion. Not a freedom FROM religion.
I'm an Agnostic that likes Heathenism but regularly attends a Luthern Church and am raising my kids as Christians.
God is bigger than any one flavor of religion. If you don't want to follow a religion, or think it's all nonsense, that is up to you. Being militantly ANTI-religion trips over that whole "freedom" thing and will more than likely not end well for the Atheist.
I'm curious, what negative consequence do you anticipate for the atheist in this case?