I cover my car all the time, to keep scratch causing dust off of it, and because of where I park it, from people randomly rubbing against it. I always dust the car before I put the cover on and make sure it is clean. The cover is shaken often to get any dirt off of it. Reasonable percautions should keep scatches to a minimum. Most are caused by imporper washing, waxing, not 100% clean cotton towel-microfiber is best, etc...I'll take the risk of covering my car for MY situation as it would have many more if I did not.
Final Word: We all love that show car look, however, if you actually drive your Vette, like me, it takes lots of time and energy to keep it looking like a show car, and scratches and other stupid stuff are going to happen, but that is why we have buffers, and compounds to take scratches, swirl marks, etc...out. If you need to cover your car, DO IT, just dust it off before you cover it and keep the cover clean as possible.
FYI, Black is absolutely fabulous clean, but it stays that way for about 5 seconds. Especially in my neck of the woods. My Ruby Red is ok, silver is best for keeping something clean. Doesn't show dust, scratches like darker colors do. Light Blue isnt bad either.