It's the "permission" thing that gets me--it implies that such permission could be denied, and I don't think that's right, not to mention being practically unenforcable. By posting content to the Web, I think inherent permission is given to link to that content. If bandwidth is a question, the streaming audio could be moved offline or offered on a subscription basis. (For example, registration is required to view content on the New York Times Web site, and I'm not registered, so links to NYT stories go nowhere for me.) Furthermore, I was unaware of the site's policy until I stumbled across it on Blogdex; I've linked to NPR content before never imagining the policy existed because it's frankly counterintuitive.
I don't plan to ask permission from anyone to link to anything. I have no problem with courtesy notification, but the concept of hyperlinking is inherent to the World Wide Web. The possibility of being linked is the price anyone pays for whatever benefits they feel their Web presence brings.
Update: Wired News reports on the furor; the story quotes NPR ombudsman Jeffrey Dvorkin as saying the organization "just wants to make sure that the links are appropriate to a noncommercial and journalistic organization," a position I can understand, even if I don't condone their policy. He also said a clairified policy is currently in the works. But the Wired story also appeared to quote Dvorkin--it's hard to tell; there's no attribution at all in this paragraph, although preceding grafs do name him--as saying "we want to keep track of who's doing it."
Update 2: Cut on the Bias calls me out for soft-pedaling the issue:
Equivocation, Greg, you have equivocation. NPR is unequivocally wrong in this. If you can't take the bandwidth hit, stay off the Internet. And if you're wanting to make sure "the right people" are linking you, stay off my earth.
Fair enough. Let me make myself perfectly clear: NPR is indeed unequivocally wrong. The essential nature of the Web implies that material posted to a Web site may be linked by anyone, any time they please. Permission is never required, and as long as said link is not misleading or fraudulent, the linkee should have no power whatsoever to force the linker to remove the link.