You could buy those surfboard pads they make for roof racks. There are a bunch of companies including Yakima and Thule. If you're not too concerned with looks, you could always go to Home Depot and get some pipe insulation. You know... those long foam tubes that you cut to length?
Either way you go, you'll probably have to cut the pads to fit. Zip ties would fasten it all down.
By the way... Nice truck! Like the color too. Is that like a cream color? Did you have it painted? If so, did you install the moulding along the side or is it all original paint?