I kept having issues with my transom getting all scratched up... so I just got the 3M scratch protection film on my boat a few weeks ago and it is really amazing stuff...its helped prevent lots of major wakeboard dings already! And it actually made my boat look better than it did before. I definitely recommend it!
I suspect most of the scratching is during using the boat. On the other hand if some of the scratching occurs when the cover is on this is an idea. I put this transom cover on and it works great.
I got it on ebay, search "transom scratch protection," "boat scratch protection" or "trailer scratch protection" depending on what you want. They have different kits you can get on there.