I have to stick up for Jackson here. It's the principle of the thing. Hollywood is notorious for stiffing actors and directors of the cut. Alot of them will take a reduced salary in exchange for a cut of the profits. It's a risk for them because if the movie tanks, they don't get paid. But then the studio will use creative accounting to pretend there are no profits.
A studio exec takes a college buddy out to lunch, and that goes against the "profits" of the picture. Security guards at the studio where it wasn't filmed get charged to the movie. All sorts of creative ways to screw the talent. If Jackson signed a contract for a cut of merchandise etc and they stiffed him, they should pay him. Period.
I think one of the most famous incidents of this is Forrest Gump, which, IIRC, made no profit. The writer made nothing.
For the record, I really worry about Peter Jackson directing The Hobbit. It has to be of a very different tone. Even with some of the problems with Jackson's presentation (and I think by the time they were doing film 3, they could have added a scouring of the Shire version to a special DVD edition) it was a labor of love. He wasn't just a guy doing a movie.