I recently bought a 2008 d22 200000km on the clock. Down the sides some one put some clear disks just above where the tonneau hooks on, and there is no visible wear, but they didn't put them on the tail gate and the paint is completely worn off. Ad the cover has definitely seen better days too.
When I bought my ute it didn't have a tonneau so I bought a genuine Nissan tonneau kit on eBay.
The kit came with those clear stick on discs to stop the back of the bungee knuckles rubbing the paint from through the cover and they work, I have them all the way around and no issues, maybe something similar can be found at Bunnings or Nissan may sell them separately.
Road King is right there is a clear laminate type application you can buy, similar to what u can get for head light protection, that should work well, it does fade and turn yellow after a few years but id say it would be worth it.
I already had them put on... Nissan did it after the first time the cover rubbed and they resprayed the tailgate. I'm having any argument with Nissan cos its rubbed thru the paint on the side of the tray