Flies can fly freely in moving cars because they are flying relative to the air inside the vehicle, which is moving at the same speed as the car. This principle is similar to how passengers can breathe comfortably in a car traveling at high speeds, while sticking their heads out the window results in discomfort due to the wind resistance. The discussion highlights the concept of relative motion, illustrating that the fly's movement is unaffected by the car's speed. The term "Galileo's Boat" is suggested for further exploration of this concept. Understanding these principles clarifies why flies can navigate within a moving vehicle without issue.