Tyler, how have you done it?
If you aren't seeing the windshield in the shot, it's really easy.
Cut a piece of plexiglass to fit the window. Then make a small cut for the lens of the camera. Tape the plexiglass to the car using gaf tape. We used a thicker piece once and attached speed rail mounts to it and the top of the car, so it worked like a hinge. We then built a small box out of the remaining plexiglass to cover the hole left by the lens and camera. On one shoot, we built a little box out of plexiglass, glued it together and used that to cover the entire camera, so no wind would come in.
Another trick I've used in the past on night jobs, is two pieces of plywood along the side of the hood (l&R)and a piece of plexiglass on top. Screw it all together which gives you the over head light looking down, but gives you a box to protect from the wind. It allows you to put speed rail on the plywood, to hang lights and gives you a lot of room to mount the camera. We tried this trick with a car in motion once and it worked really well once we put another piece of plexiglass covering the gaping hole in front. On a trailer rig, you can cover that with extra pieces of plywood if the wind is crazy. But from my experience, the half-box generally reduces the wind enough.
Now sound is always a problem with car shots, doesn't matter if the windows are up or not. Most of the time I go into a car scene knowing I'll have to ADR it. So in my eyes, the sound isn't a big problem unless you're working with A list talent and don't have the money for an ADR session. Sure, there are rare occasions where the road is super smooth, the windows are up and the camera is on the outside of the car. However, I haven't been that lucky over the years, most of the time, the roads are beat up (car shaking), windows are down and camera is inside the car making all sorts of noise. Since audio is just as important as picture in my world, ADR is really the only solution to good audio in a moving car scene.