I wouldn't use any paint over the rubber roofing material. A standard elastomeric paint will leach some toxins that you might not want in your water system.
Does the rubber roofing material need additional protection? If not leave it as is. If it does need some kind of covering then you should look outside the realm of normal paints. One alternative is to use pool paint. This is a chlorinated rubber that is used as a liner in swimming pools.
The pool paint might be a good alternative. Another might be the rubberized roof coatings that I see in the home improvement centers. I don't know if they would leach any toxins.