I don't believe that the government does. Atheism is when you don't believe in God. I think the government just... doesn't take a stance on God one way or the other when they try to leave religion out of it.
 

You said that atheism is"a belief about god" and "should be treated as a religion." If you mean about God to mean that they do not believe God exists. Then I agree with you. But as far as treating it as a religion I disagree. Religion, in my opinion, is a form of worship--be it Judism, Christian, Muslin, etc. As far as I understand Atheism has no form of worship and their disbelief sets them apart from the religious world.
 

"One problem is that people think the only way to protect the freedom of religion is the government endorsement of Atheism."

Typical strawman argument. Atheism is the lack of belief in god(s). Quote one source where anyone has suggested that the government endorse atheism. Those who understand the constitutional principle of separation of church and state know that government neutrality regarding religion is not tantamount to creating or endorsing an atheist state. If the government were to officially declare that there is no god, that would be a violation of the Constitution, as that would be taking an official position regarding "God." No one of whom I am aware has ever suggested that this be done.