This was my first season with my new Cedar Creek, the Gelcoat is a pleasure to keep clean compared to the previous units I owned having the aluminum siding. The one problem I have is the water rust marks on the rubber roof, I just can't get it clean!!
The "Works" toilet cleaner will remove rust stains from concrete, but it is VERY CAUSTIC. You might try using a very small amount on a Q-tip to see if it would work. MAKE SURE YOU HAVE GOOD RUBBER GLOVES ON. Wash it off with liberal amounts of water.
I once wiped a doorknob with a rag that had "the works" on it. Took the finish off right down to the metal in seconds. I would not use it on a rubber roof.
Nobody can see your roof, don't worry about stains.