Protein skimmers remove dissolved organic compounds which can lead to nuisance algae outbreaks in aquariums. Many dissolved organics can harbor nitrates and phosphates that are the fuel for nasty algaes like cyanobacteria, byropsis (hair algae) and dinoflagellates. Also many corals do not appreciate dissolved organics and their growth can be stunted by their presence (hence the need to remove them with a skimmer)