I have used Back to Nature Auto Strip on fiberglass doors without any problems. It is safe for fiberglass. Another good paint and varnish stripper is Multi-Strip by Back to Nature. It is also safe for fiberglass doors.
Both of these products a pretty good and much safer than strippers containing methylene chloride.
A good place to find fiberglass safe paint strippers is at an automotive paint store. Many cars have fiberglass components and the pros need a good safe paint stripper for these components.