Yes, skimmers do work in freshwater, and are frequently used in aquaculture and public aquariums. It is a question of surface area and a property of water called surface tension. Smaller bubbles have a greater surface area, and so can bind more protein per unit volume of air. And because of surface tension, it is easier to make smaller bubbles in salt water. So for freshwater, you must generally use much larger volumes of air, which is hard to do with aquarium-scale equipment. The cost is usually greater than the potential benefit, which is why so few people bother.