Good question Lynn. Looking to Albert Einstein and his theory of relativity, if you replace the fly in your question with say a cricket ball on the floor of the boot of your car, if you accelerate from still, the ball will appear to do just that, and roll to the back of boot. In fact it isn't rolling 'back' at all, it is 'trying' to stand still in relation to the earth's gravity, and it is the car that is moving forward. Similarly, you too would try to stand still in relation to the earth's gravity if you didn't have a seat -back to keep you in place.
The fly is also being affected by the earth's gravitational pull but as weighs in at about 300 micrograms that pull is very slight and if it is in flight it is more conditioned by the air pocket within your car. However if it were standing on your cars window-cill it would undergo the same force as the cricket ball but this would have almost no effect on it because of its tiny weight.