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.
Just out of curiousity .... having used roof racks extensively for skiing ... I fully understand the practicality of having them. My question is with luggage baskets and bike racks ... HOW DO YOU GET ALL THAT STUFF UP THERE ... even with skis sometime the height can make it a bear to get them up and in the right place ... but a 18 or 20 in bike or a 30 lbs suitcase would seem a pain to get up without damaging the car ... definitely, I would guess, not a one person job ...
This website has a rooftop protector you can get for their pouch type carriers. The Sherpak Supermat Roof Pad is only $12 and fits in between the pouch and the roof. I have a different brand than the one at this site but it is similar. Benefit of the pouch type of roof rack is that it folds (roughly) into a 10" by 40" by 2" thick package. This makes it far easier to store than a hard shell type of carrier. Also, the one make sure you get one that has tie down straps on the sides as opposed to only the front/back. If strapped on and loaded properly, you shouldn't need to buy the roof rack accessory that adds the front and back bars. Some of these are more waterproof than others but we put anything that we don't want to get wet in garbage bags as a precaution. We have not had any problems even in huge downpours.
Head over to your local car parts store and see if they have come clear (or you could go with any color you like) thin strips of body side molding. You can apply it to the ridges on the roof to protect when you load up suitcases and such. Doesn't protect the valleys between the ridges, but at long as the objects are flat it works pretty well. If you get clear, you won't even see it.
I really wish Honda would offer a solution that looked and worked better, but the clear molding isn't a bad compromise.
Cheaper Alternative to the Sherpak Supermat Roof Pad ($12)
I looked at the Sherpak Supermat Roof Pad ($12), and I found a similar product and a bit cheaper. I am using the same pad used under a carpet to avoid it from slipping and sliding when on a hardwood surface. You can get it from Walmart or Target.
By the way, I posted a question earlier about loading a soft carrier on my roof. How much weight can I put on the carrier? Is there a steel bar that helps prevent my roof from caving in or denting because of the weight of the carrier?
Our answer was to get a small/inexpensive ($100.00) Yakima rack and a Weather Tech bag to carry our stuff (remember George Carlins talk about stuff?) It looks like this and cost only about $170.00 total.