Originally Posted by Clam

My answer is, "maybe". The fly's reference frame is the air in the car, meaning that the fly is positioning itself relative to the mass of air in the car. When you hit the brakes, everything in the car will move toward the front because everything in the car has forward inertia while the car itself is rapidly losing inertia. The air mass in the car will slightly compress at the front of cabin and decompress at the rear, but since the cabin of the vehicle is completely filled with air, there should be no huge air currents created. The fly will probably move forward somewhat. Will it hit the windshield? Maybe, but I kinda doubt it. Of course, this is all predicated on the idea that the windows are up.

But hell, what do I know? My degree is in computer science, not physics...