Why would you do that? If your cars standing in the rain with the cover on top, water will seep into the car cover. Car covers cannot absorb this water and since the water wont have any way to evaporate, it will start etching at the clear coat. Keep doing this for a few months and you will end up with mater marks and clear coat failure. Thats why, you always let the car air dry for a few minutes even after you dry the car before covering it up. Water left on the paintwork will do you more damage than a small bent plastic antenna.
Almost all of these cars have the screw-able rubber antenna. You can simply unscrew it when covering the car up. Dont go around ripping holes in the car covers.