Are there any manufacturers that make a pad/mat specifically for SUV's with the roll down rear window that will protect the paint/window seal from hauling a kayak?
Hauling a kayak inside through the rear window? Most kayaks are too long to do that, so they are usually put on a roof rack with tie downs at the front and back. The rear tow hitch receiver is excellent for the rear tie down.
Edit: Both Yakama and Thule make kayak racks for the roof.