On my 2009, i had the Line-X spray in liner & i just tossed things in it.
I had to have the spray on redone on the tailgate, but that was because i trashed the tailgate.
With spray in liners, if you dent the bed, the Body Shop has to remove the spray liner to fix the sheet metal. $$$
Bedrugs are nice, they are very durable & easy on the knees, which is grand if you have a camper shell, that crawl around on.
Bed Mats are good if you are not hauling rocks or Fire Wood, that could dent the Bed Walls
I would remove anything like a rubber Mat at least once a year, if i lived where it rains on a regular basis