It's not generally the drivers fault, but a combination of Jeep engineers, age, and the rain. The rain can find it's way in through various typical weaknesses (windshield gasket, A/C drain, rear window seal, door seal, firewall holes, etc) and if it gets in, it can't get out. The insulation soaks it up and floor rot is inevitable if nothing is done about it. :(
The bed sides have a design flaw where dirt and debris can get stuck up above the wheel well on that little shelf and that attracts moisture and bed rot is inevitable.
The bottom of the doors usually rot due to dirt getting in and plugging up the drain holes, causing water to stick around and rot them out.
The rockers, well, I'm not entirely certain about them. There's probably more than one way for the rot to start and once is starts, it goes downhill fast.