I'm not sure exactly what you want to protect against. Is it getting stuff onto your roof, or protecting the roof once it is up there?
If it is while getting the stuff up there, the only thing I have seen is a roller device that you stick on the rear edge of your hatch using suction cups. You can then roll your kayak, canoe or other large long object onto the cross bars using this thing as the guide, so that the object does not scrape along your roof top. You then take it off before driving and store it.
If it is while it is up there, then it just depends what you are planning to put up there. THere are many types of roof rack systems, each one focused on a particular application. If it is luggage, then as N_Jay said, a basket is best. If it is a kayak, get a rack that is designed to hold a kayak. But whatever it is, if you get the right rack, what you are putting on the rack should never rest against your roof top. Except as you struggle to get it up there, which is why I am assuming it is the other case. That is where I do all of the damage to my roofs.