I'm an affiliate of many poker site. You sign up through me to play at Party (for example). Party gives me a % of the rake you generate. I, in turn, give a percent of what I earn back to you. It's win-win-win.
Sometimes the huge affiliates are paid more so they are able to offer their players back MORE than I earn in TOTAL. This sucks for the small affiliates like me, but what can you do?