One responce and you decide no one likes them?
(Oh, and I gather that you are talking about Affiliations?)
We have used them in a game where I have been a player. An order approached the PCs for assistance (actually 2 rival ones did, we initailly didn't agree to help either but decided in the end that the agenda of the one was better for our interests than the other) and after an adventure or two several of the PCs had a potential affiliation score. We decided that the group, which was a benevolent order of paladins, clerics, fighters, etc, would grant the lowest level benifit of the association to the the PCs as a bonus for their assistance but that to recieve any of the higher level ones unless a PC actually joined. My cleric did and soon rose in ranks as we completed an extended quest for the Order, incluiding a minor magic item and +1 weapon.
Overall it made the organization more interesting. They became more than just another big group of NPCs that wanted the PCs to fetch or destroy something. I will certainly use them in future games I run, and I hope more show up in the current campaign.
I do think that I will either try to interest the PCs in an organization to which they can all belong, or at least support, or use very specific non-competing affiliations that would allow there to be many in a single group. I wouldnt want them to develop into somethign that could be disruptive of the group. But that could happen with or without scores to go along with them.
If you like to use various NPC organization in your game and want to encourage players to interact with them or even join them then Affiliations are an excellent way to do so. If on the other hand you dont really care about the PCs doing so then I wouldnt bother, but not becuase they are hard to keep track of but because they wont add much to your game.