Like most minorities, atheists face discrimination from religious people because they don't understand them. Religious, specifically Christian, people in America often cannot fathom the concept of somebody believing in something other than their own. They often see them as theistic devil worshipers, or think that they're in denial the existence of their God. I personally have been harassed for "worshiping the Devil," or something, when speaking to another atheist student about our beliefs. The ironic thing is, we were in science class.
In some countries Atheists don't have the right to even live (almost all of those countries are in the Middle East or Africa) much less be equal. Here in the United States atheists can't run for political positions in several states and there's no way an atheist candidate would ever be elected as president. As I say in my "beliefs" section, religion and morality are two completely separate things but everyone thinks they're the same. It seems to be worse in modern American society to be an Atheist than it is it be gay or even a person of color (both of which aren't bad). Atheists aren't treated equally and probably won't be for many decades, it's a shame :(
There are states in which atheists cannot hold office.