Yes, my factory running boards do a great job protecting the side of my truck.
At some point on my 4200 mile camping trip to Yellowstone and back over two weeks, I ran into black tar on the road in one of the "many" construction areas along the route. I did notice it until I got home and what I found was a thick coating of black tar on the underside of the front fender lip and the back quarter panel of the truck all the way back onto the rear bumper and as high as the Tremor sticker. It took quite a bit of soaking it with goo gone and using a micro fiber cloth to remove it all.
The side of the truck between the front tire and rear tire was clean, as the running board blocked the tar from spinning up onto the doors and the front half of the bed. I guess I could have used a rear mud flap, but I really do not like the looks of them, so I did not want them on my truck.