I don't know about the bedrug, but most bedliners do long term damage to the paint. Now matter how well they fit, the vibration of the truck in motion and cargo bounced off the surface as it is loaded and unloaded will eventually rub spots in the clear coat, and then the paint eventually. Dirt gets trapped underneath (like a front-end bra) and then just sandpapers your finish. Moisture can also get trapped underneath, even with the tonneau, and eventually cause rust and other problems.
Unless you're trying to preserve the truck in total originality for some future generation, I would recommend a spray-on liner. I had mine done by Line-X and was very pleased with the finish and with the care they took with the truck while working on it. I had them do the bedrails as well, but only half as far out as they normally do. That way, you can't tell any difference at all with the tonneau closed but you're still protected on the bed edges when you need to drag something over the side or tail, or if something big sticks out while you're moving it.
