My brother and I have used car covers for a long time. Our experience has been good, if you use a car cover that is breathable. If you used something that is not breathable, like a plastic tarp, you will mess the paint up for sure. The humidity needs to be able to get out.
The same thing happens with a bra. When it gets wet, it will mess up the paint. Take it off the car, and let it dry out before you put it back on the front of the car.