I think its all about water quality, is protein skimmer going to help in a tank full of BBGs? probably not. In a tank with large messy puffers and big predators, ? yes, because IMO anything that you can do to get crap out of the water before it breaks down is a plus.
What kind of skimmer is it? Not all of them are up to the same quality as others. You should try running it only once a week. I know Sabby runs one on her tank, its a large aquarium with large fish.
I am running it on a large aquarium, with Monos and Scats. It is not a high quality skimmer, however I do have to empty the gunk out every 4-5 days. I just never see it working, but I know it must be or I would not have to empty that foul stuff every few days. Since I have been running it, my algae has been reduced and my water quality has improved. IMO the skimmer is worth not having to do so many water changes, saves a little on salt. I do however undestand the importance of water changes, and by no means is this an attempt to not have to perform them, It just gives me a little more time between them.