You didn't mention whether or not if you were going to do it yourself or have it done. Through carelessness on my part, I have had and damaged both types over the years on tree branches and repair was about the same on both. With your unit being an '06 and a rubber roof will have more pliable-ability, I would go with a new rubber sheet. In spite of the cost, nowadays, I'd opt to have it done. I did do a replacement on a metal roof on a old Scottie semi-tear drop travel trailer years ago that we use as a closet/storage shed for DW when parked for a long term stay when we lived in a Toyota Dolphin. It required replacing all the plywood underlay and most of the 1 x 1 cross braces (rafters)due to rot . That was the majority of the work. Even though I bought corrugated aluminum RV roofing basically cut to fit on length and width it was still a lot of work. If you are going the DIY route, the link is a video on a guy who did it himself.
http://www.youtube.com/watch?v=tyQ8t5vXaUI
Stan, Shirley & 2 Schnauzers
RV: 2014 Itasca Sunstar 35F
USAF Retired, Life Member: VSPA, VVA, DVA,VFW