There are some limited circumstances in which you should use a car cover, such as potentially going out of town for a long time and being forced to park your vehicle outside where it could be damaged by bird poop, hard water spots, and other contaminants. Ceramic coating are not impervious to damages of these types. So, we might reluctantly agree that car covers are appropriate in this situation, even though we generally dislike using them.

In general, your paint is fairly susceptible to scratching, even if you have ceramic coating on it. Clear bra/paint protection film will protect against these scratches, but ceramic coating will absolutely not.

 When you use a car cover, it is almost impossible to keep the underside of the car cover as well as the surface of the car perfectly clean at all times. When there is dust or debris trapped between your car’s clearcoat and the car cover, it is no different than rubbing your car with a dirty rag (maybe even worse, in some instances). This is whether or not the car is inside or out, as even inside, the car cover may move or brush against the paint.

Outside, the situation is far more dire. Even a well-tied down, perfectly fitting car cover, will move in the wind. The tie-down methods as well as the car cover itself will move, abrading the paint and removing any ceramic coating from the surface. Remember that ceramic coating creates a semi-permanent bond with your paint, making the only way to remove it is with an abrasive material. A car cover with dirt trapped between the underside and the ceramic coating will certainly act as that abrasive material, just like a compound or polish will abrade the ceramic coating off (or an automatic car wash brush). 

You would think that you cannot get dirt between the cover and the ceramic coating if the cover is on, but that simply isn’t the case. It’s bound to get some dirt, however small, under there. And even if it doesn’t, the constant movement of the material against the ceramic-coated surface (or bare paint surface if you have yet to purchase ceramic coating or clear bra) will damage the paint.