Protein skimmers use air bubbles to attract and export DOCs (Dissolved Organic Compounds) from the water column. As Chris pointed out fish fesces is an organic compound, and while a protein skimmer won't remove the solid form of feces or detritus (eg. excess food), once these organic compounds begin to rot or decompose, the venturi vortex of the protein skimmer creates bubbles to which the DOCs attach. Cellulose is one of the major DOCs that is removed.
The DOC covered bubbles are forced into a collection cup thus removing them from the water column. If you go to an shore line you will see sea foam which is the natural process a protein skimmer replicates.
Ciao,
Craig