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I think Harp did a pretty good job of explaining it. Although it is really vortex shedding 
that causes the rhythmic pressure changes. The shear forces in the air close to the open 
window cause alternating vortices to emerge. You can tell this is the case because vortex 
shedding resonates at the objects natural frequency and when one window is open the car 
almost always makes the sound (provided it is traveling fast enough to create vortices). 
However, a car with both windows open does indeed have a resonant frequency. The difference 
is that it is harder to get a standing wave to propagate in the interior of a car because 
of chaotic flows within the cabin and the fact that you have two windows vying to hit 
the natural frequency at the same time. Most of the time the vortices will not be in 
sync and will not cause a resonant frequency to be excited, or simply cancel each other 
out entirely. A car with one window open will have a resonant frequency twice as high as 
a car with one window open as well. Higher frequency states require more energy to excite 
which also helps to explain why both windows open often does not cause the harmonic 
frequency to be excited.

From here: http://www.fluther.com/56579/whats-that-weird-flutter-in-air-when-only-one-window-is/