I have to call foul here. First of all, Jonathon Coulton previously had permission to perform the "Baby Got Back" song. Second, if a melody is important to the creation of what could be considered a "unique work", the original rap song had no discernible melody, except for a bass track that you could probably reproduce with your mouth no matter how unmusical you are. Jonathon Coulton created a unique melody to "Baby Got Back" and he changed one line to say "Johnny C's in trouble," referring to himself of course.
Now anyone creating a cover of "Baby Got Back"---and make no mistake Glee and Fox have hordes of talented musicians to choose from. See how "Piano Guy" just pops up out of nowhere? --- could create a new version with a unique melody that is different and distinct from Jonathan Coulton's version. Are you familiar with the "Jeopardy" Theme Song? Ever hear it used in a cartoon, but it's not the original tune. Notes go down, instead of up, and it's only vaguely familiar? Fox, in this case, used EXACTLY the same melody as JoCo, down to the note.
Lastly, JoCo's version has a different tempo than "Baby Got Back". There's a reason it's over 5 minutes long, when the original song is like 3 minutes something. The Glee version, while they could have sped up the tempo, or slowed down the tempo, is exactly the same.
Now I won't go into possible "duck" samples, or questioning the exact same use of the banjo, but Glee's version of "Baby Got Back" isn't a cover of the original Sir Mix-a-Lot's version, it's practically a note-for-note copy of JoCo's cover: same melody, same tempo, same words that JoCo changed referencing himself, and using exactly the same instruments and general feel of the song.
Fox has some giant balls on this one. I don't know why they bothered to change the vocals at all, personally, if they're going to steal the entire song in the first place.
-D