Are you refering to do they take a cut? The answer would be no, that is totally unethical. Good affiliate managers look after their affiliates and work hard for them. Affiliate managers are just good marketers.
It’s customary for anyone in sales, including managers, to be compensated for production in the form of commissions, overrides or bonuses. There is nothing unethical about it. Without incentives production is generally low.
When I was an affiliate manager, I got a percentage of my affiliates’ revenue. Lou’s 100% correct; it’s a totally standard thing. (Doesn’t have anything to do with being a pyramid scheme though.)