Why do some people interpret separation of church and state as state-mandated atheism?

I understand that the Constitution says that Congress shall make no law that establishes a state religion. I've been studying American history for a few years and I know quite a bit about the historical context of separation of church and state. The founding fathers put that in the constitution so that one denomination does not take over the government and leave the others out (as was the case in Europe at the time). But one thing that it does not do is separate religion and politics. What puzzles me is when atheists say they want separation of church and state, when in reality they are asking for separation of religion and politics (something totally different). Constitutionally, if the majority of Americans feel that gay marriage is bad since the Bible says so, they have the constitutional right to ban it. With all of this in mind, how is it that some people can deny the original meaning of the term "separation of church and state".