This. When your mass is so small, you live in a very different world than we do - momentum and gravity are tiny forces on you, but others such as air resistance and static are huge. Additionally they don’t have the sort of inner-ear positioning system we do - so no real sense of “up” and “down” that would be recognizable to us - so probably the inevitable tumbling motion as you are sucked out of the window would not be disorientating to the fly the way it would be to a big animal.

So the answer is they will likely be fine. From their point of view the blob of air they are flying around in gets sucked out the window and they are just traveling in it. I imagine they would notice the acceleration, but it’s a tiny force on them. The sudden distortion to the block of air (being stretched out to fill the sudden low pressure zone outside of the car window) would be a big deal to the fly, but I don’t think enough to damage them.

Source: idle speculation, and a long standing interest in cats surviving huge falls.