That throbbing base sound aka "side window buffeting" was a very interesting topic to research and very complex. I consulted with a couple engineers and found lots of interesting information on the subject. This video condenses it down.

The video gives a simple description of what is a very complex scientific problem. That is why cars still do that–engineers have a hard time completely eliminating Helmholtz resonance. The interaction of windows, A-pillars, B-Pillars and the aerodynamic shape of the car creates a huge number of variables.

What I call "eddies" in the video is actually called Vortex Shedding, a phenomenon that happens whenever laminar flow disrupted by a "bluff" or non-streamlined object. There's a fun little fluid dynamics simulator you can play with on this site that I used to make part of the animation that illustrates this very well. http://physics.weber.edu/schroeder/fl...

Here is a page (http://bit.ly/1XFOtmf) that overviews how their CFD (Computational Fluid Dynamics) software helps engineers solve the buffeting. Interestingly they offer a slightly different explanation than just simple Vortex Shedding. They say interaction between the A-Pillar and B-Pillar pushes the eddies into the passenger compartment. But again, this is could be because every car design is different and causes different effects. That is why in some cars rolling the rear window down causes the buffeting instead of the front.

The reddit post in /r/AskScience (  / youre_driving_and_you_have_only_one_window...  ) goes into very mathematical analysis of the exact causes and science behind the Helmholtz resonator.

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