Use plywood to protect it.....
Seriously, these roofs are made to be out in the weather, why do you think you need to "protect" it with something?? If anything, I would look at a dealer's parts dept and find some spray on UV protectant and check the instructions to see if it says safe to use on vinyl.....
Steve and Vicki
2011 Dodge 3500 CTD Outdoorsman
2013 Columbus 320RS-ITS HERE!!