Sometimes it's just a matter of wanting to avoid taking a lot of time and trouble to defend yourself against a frivolous lawsuit. For example, when Weird Al parodied James Blunt's "You're Beautiful" as "You're Pitiful," he phoned up Mr. Blunt and asked permission, because Al's a nice guy like that. Blunt gave him permission, but his record label (who actually own the copyright) objected and threatened to sue if Al put the song on the album.
Now, Al could have gone to court over it, and he almost certainly would have won. But that would have been a lot of hassle, so instead he just released the song for free over the Internet. Al's fans got the song, it made for a nice free promo for his album (which I very much doubt suffered any loss in sales over one song being missing anyway), and Atlantic Records backed down. Everyone wins except the dirty bloodsucking lawyers. (-: