I understand exactly what you're describing and I wish I had put these Velco strips on the sides of my hull when my boat was new. The same kind of rubbing wear can also occur in the water if you have your Amas folded in; like at anchor or dockside etc.
I'm not quite sure what material you could use that wouldn't attract some kind of dirt and yet still act as a good separator between these two surfaces. Prior to using the Velcro strips, I experimented with foam, but discovered that it too was abrasive. Scraps of rug seemed to work well, but looked kind of crummy and were always getting lost.
Pictured below is the 2 in. Ultra-Mate Industrial Heavy Duty Sticky Back Velcro Tape (using the soft side out) that seems to be working the best so far. It's been on my boat for over a year now with no signs of peeling off. That's what I recommend.
This is how I installed it on a friends TI.