Gotta think of it in terms of mementum transfer. The more secure something is to another object the easier the momentum with transfer. When the car is stopped the windshild is strong enough to anchor the air, to keep it from moving forward whent he car stops. The fly's wings beating anchors the fly to the air strong enough so that the momentum of the fly moving forward is stopped by the air. If the fly were to stop beating its wings at the exact moment the car stops the fly may very well shoot forward.
If the fly is sitting in the sill of the rear window and the car stops it would also shoot forward the same way that tissue box would unless the fly's feet are able to secure it to the window sill the way the fly's wings would secure it to the air. Just like your seatbelt secures you to the seat, which is secured to the car.
Also keep in mind the fly weighs very very little, so the amount of force that is required to keep it from shooting forward is very very little.
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We Must Dissent.
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