[I am far from an exprt, but I have read alot about this from a number of different sources and I keep getting back to the idea that low nutrient water is the first key to succesfull coloration and maintenence. In high nutrient water they reproduce, they also can produce darker or light pigements from golden to brown depending on light levels. The zoozanthelle act like a mask dominating the color of the coral.
Here is a quote from Eric Boremann regarding the pigments we are typically concerned with:
"Finally, and most likely to be of interest to aquarists, are the light-related fluorescing proteins. Some corals produce these in response to high light and they act as photoprotective shields, such as some pink morphs of Pocillopora damicornis and some blue morphs of Acropora spp. Other corals produce them in response to living where the light is very low where the proteins act as photoreflectors, such as in Trachyphyllia geoffroyi, Cycloseris spp., and many faviids.
It has recently been found that some species seem to produce them for no currently known reason at all.
The fact that not every colony of a species responds the same in terms of fluorescing protein production under the same light conditions also suggests that there are specific genetic components invovled.
The overall coloration of corals is therefore a complex function of genetics, light-related fluorescing proteins, dietary derived or metabolically produced tissue and skeletal pigments, and their combination with the various hues of brown that mix into the palette in all corals with zooxanthellae (a function of both light and nutrients, primarily)."]