One of the things I learned when I did a deeper dive into PBS affiliate funding and scheduling yesterday is that local affiliates are sometimes able to acquire and broadcast material at essentially no cost. It works like this: an independent producer approaches the affiliate and says "Would you like to broadcast a documentary about X?" The local affiliate says "Sure, but you have to find the funding, because we can't pay you for it." "Fine!" says the independent producer, "It just so happens that company Y & foundation Z have agreed to underwrite the production in exchange for a funder credit announcement at the beginning and the end of the program." "No problem!" says the local affiliate, "So long as your content complies with our guidelines, our charter, etc etc." And the thing gets done.
Also, re fees: I believe that the fee schedule takes the size of the market into account as well, so that say, New York's affiliate might pay a higher fee than an affiliate in a smaller market would. I need to confirm this.