I've bought 7 RVs since 1989, none of which, other than the 31C Itasca I bought last June, and will never use myself, had fiberglass roofs. All but a 1997 Coachmen Class C, which I bought in 2008,and the 31C were bought new.
I've never had a problem with a rubber or EPDM roof or whatever roof my 1989 Coleman pop up came with. The only roof related problem I had was with a 1995 Four Winds Class C which came with an aluminum roof. Within the first year, electrolysis started in the cabover roof. My selling dealer pulled off the aluminum roof and replaced it with a rubber or EPDM roof (I forget which), which Four Winds covered.
I did replace the rubber roof on my 1997 Coachmen in 2012, because it was looking a little worn, and my son does that kind of work for a living, so it was cheap enough. That roof was 15 years old, and could have lasted a few years longer, but I decided to replace it.
I would prefer a fiberglass roof, but would (obviously) never consider a non fiberglass roof a deal breaker.
2014 Itasca Spirit 31K Class C
2016 Mazda CX5 on Acme tow dolly- 4 trips ~ 5,800 mi
Now 2017 RWD F150 with a drive shaft disconnect