I had a drop in in my little Toyota for 150,000 of its 250,000 miles life--so far. They do abrade the paint, things slide around in them and they can cause rust. I took mine out after I saw it doing damage to the paint after it had been in a few months and reprimed the abraded areas in the bed. I then took the thick foam tape used to seat bed caps on the truck rails and laid several strips in the bed. The foam seated in the liner and it stopped rattling around after that. Auto shops have a clear tape which is used for rock and scratch protection. It is a tough film that is clear and can be laid on the truck bed rails where the liner overlaps. The foam can be used there also as well. I think the under the rail type is better with a seperate rail protector is best. On the Tundra, it got a spray-in that was color matched, I like it better--and since it is not a WORK truck it is more than sufficient and very durable. Bed mats tend to blow out at high speeds. My friend with the hot rod Chevy says his mat is a speed indicator, it lifts up and floats around at about 90, when I was in behind him on the bike I saw it do just that. I had one in the little Toyota for a few weeks, it would not go 90 but it was windy and it went away, don't know where it is. I have also seen people use those heavy stall mats cut to the shape of their bed. They are tuff and heavier than most mats.
That clear tape is good for your side panels and areas of the hood that are exposed to gravel. There is a new type out that is usually pro installed because it can be shaped and stretched over curves forming an invisible shield. The last stuff I used was a 3M product I think. It would be avaialble at the types of stores that service auto body shops and supplies--not Autozone or Pep Boys.
I have also seen people use large pull rivets or bolts at the corners of the liner to hold it down tight so it does not rattle around--it is the moving around that wears the paint and then causes rust. J