Why not just lay the bike inside the bed? Throw a furniture pad down in the bed and lay the bike on that pad?
For one bike, I just lay it down. My 1988 B2200 had scratches in the bed when I got it in 1994, and here in Arizona they don't rust. For 2 bikes, I lay a piece of old carpet over the tailgate and have the front wheels over the tailgate; or I use my old 4-bike Reese bicycle carrier that I bought for $90 at K-Mart in the 1990s, fits into the 2" receiver I bolted to its bumper.
My 1998 and 2004 Frontiers each had factory plastic bed liners when I bought them used, and I've never looked under them. At least in Arizona there won't be rust under them !!!