"Atheists are treated worse than Muslims or Gays today."

Probably correct there. That's why their rights need to be respected. Both of the other groups you mentioneded have organizations that come to their aid when their rights are infringed upon. It seems that by nature - athiests don't belong to groups that have the power to protect their rights. The ACLU comes to mind - but the answer to this and other problems where rights are trampled is to organize.