Hi Les,
The 2004 Towlite we upgraded to has a rubber roof. I've gone over the roof in detail looking for delamination and any other evidence of failure, and have found none. This year we cleaned the rubber and applied a UV treatment, and I suspect its the first time any attention has been paid to the roof. We bought from an elderly couple who weren't into maintenance.
After considerable reading and other research, I've found that, in our dry climate, providing only "approved" chemicals are used or applied to the rubber, it should stand up as well or better than fiberglass, although probably not as well as aluminum. Petroleum based chemicals can cause serious issues, as will a number of cleaning products, and waxes. Certain caulks are recommended and others aren't. So if you get the rig with the rubber roof, read the labels of any product you're thinking about using to see if its okay. That's the big difference, as almost anything can be applied to fiberglass or aluminum.
I've read that a rubber roof can be replaced, if needed, at much less cost than either fiberglass or aluminum.
Just waxed our trailer this week, and sure enough, the bottle stated a warning to keep the product away from rubber roofs. I did!
Jim