Yes......these plastic bedliners do create a bad scenario where the rubbing can scratch the paint beneath it and start to let moisture attack the bare metal where it is rubbing. If the truck was used to haul sand or dirt anytime, then it will find it's way under the bedliner also, and add to the carnage.
That said, I actually like the original Mazda plastic bedliners. I'm in the construction industry, and tend to haul heavier items in my trucks.......the bedliner helps keep the heavier things from denting the sides and floors of the steel bed. You can actually line the floor with a thin "protection mat" that is made of the plastic that is used sometimes in packaging items when shipping. When I bought my 2002 Chevy Silverado and bought a plastic BL for it, there was a precut protector that I bought from GM that went under the bedliner, to help protect the paint. And it actually worked pretty good.......but I should have bought several of them and maybe replaced it every 8-10 years, and it would still look perfect under the BL now.
On my red Mazda truck, I removed the BL and spot painted POR-15 over the areas that were either rusty, or where the paint was rubbed off. Hopefully it helps in the long run. In North Central Florida, we do pretty good as far as not rusting like you see along the coastal areas.
I'll need to look for the pics after spot painting the POR-15 on the areas that needed it.
