Interpreting microphone output signal
Sound behaves (more or less) like a wave. When the positive peak hits the membrane it is moved in one direction and afterwards "sucked" in the other. Just as waves on the beach do. 
Each positive peak generates a equal negative peak (in a perfect world...). Superimposition of different waves makes it hard to see this directly.

The average is not necessarily the atmospheric pressure, but is a combination of it in combination with the property of the electrical circuit of the microphone.

For your fft you have to consider positive as well as negative values. However, you may want to get rid of the average value if you do not care for very low frequencies.