First connect your AirPort disk directly to your Mac, and set up Time Machine to use it. If you want to let it back up now, that's fine. Alternatively, you can stop it and let it back up when it's plugged back into the Airport Extreme Base Station (AEBS).
Time Machine creates a file in the root directory of the disk called .1234abc5678 -- the exact name will differ on your Mac. It appears this file has to be in the root of the network shared directory. In my case, I use user accounts to manage my AirPort disk, so the directory that it actually shares out is called /Shared on my disk. So I simply move the hidden .1234abc5678 file, or whatever it may be called, to the /Shared directory. If you let Time Machine back up while plugged in locally, you will also have to move the .sparsebundle file to the /Shared directory.
Eject the disk and plug it back into the AEBS and mount it via AFP, and Time Machine should pick it right up. This method should work for any AFP share, not just AirPort disks.
[robg adds: I strongly advise that if you're going to use this hint to enable TM backups to an AEBS disk that you have an additional backup strategy, preferably something local and known to work well. It's possible that Apple disabled the AEBS Time Machine feature due to issues with the integrity of the backups -- not exactly something you'd want to worry about in your only backup solution. I haven't tested this one, but at some point, I probably will with a NAS that mounts via AFP, just to see how well it works.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20071026075201634