I've neither read nor watched Fight Club, but as for Ra's al Ghul and the League of Shadows from Batman... remember, Batman became an exile and was hunted down by them because he betrayed their orders. Dark knights follow no orders but their heart's - having an organization they answer to undercuts this ideal. (Of course they still protect the innocent, but typically do so on their own terms and only because it's what they want to do. You could say they selfishly pursue selflessness, like a certain visual novel hero.)
Having a master doesn't mean there's an organization, it just means there's someone able and willing (however grudgingly) to teach would-be dark knights the art. Look at the Sith from Star Wars - after Darth Bane declared the Rule of Two, there was just a master and a student who kept their activities on the down low to avoid suspicion. It's better that way; dark knights answer to nobody, so nobody loses anything if they're killed or captured. Except the knights themselves. So while there might be other dark knights, we don't know of them, and it's better for everyone that way.