I have a 1993 HR Navigator with a rubber roof, and it has never leaked or had a problem. The Navigator is the top of the line coach from a very large RV manufacturer who also uses aluminum on some of its products. Our 1989 HR Imperial had an aluminum roof that also never leaked or had a problem.
So, having a rubber roof doesn't mean the rig is cheap or the roof will leak. Having said that, I did have it coated with a non-petroleum based paint in 2003 to help preserve the roof. RV manufacturers do not recommend coating the roof with anything but just keeping it clean using a soft brush and mild soap.
Holiday Rambler Navigator DP, Hummer, and Honda VT1100C Shadow