He didn't do quite so well with the big book of The Hobbit!
LOTR was cut down from the original material to make it three films. The Hobbit was expanded massively to stretch it to three films. As Jackson has said many times of LOTR, Tolkien knew what he was doing, and every time they tried to deviate from the book, what they did was worse. Where they had to make up new stuff for the Hobbit, it came up worse, where they stuck to source material in LOTR it was great.
We saw the same thing with the last two seasons of Game of Thrones (worse when they ran out of Martin's books to follow). Look at Ridley Scott. Great with Alien (Dan O'Bannen and Geiger to follow), and The Martian (copied directly from the book), Bladerunner (Dick's book), but terrible with Prometheus and Covenant where he did his own thing. JJ Abrams and Rian Johnson terrible at everything they write themselves.
There's too many directors who think that they are writers, and that the story is the least important thing of the movie. They want the credits, the residuals, the control of the projects, but they don't know as much as they think they do about writing narratives and characters. As we've seen in so many recent movie failures, directors are great at the actual filming and visuals, the translation to a film medium, but often quite bad at creating the source of that material in the first place.
Something like Dune doesn't need every single little thing as per the book. Just like LOTR, you can leave some things out. Dune only needs a core cast of characters against the massive backdrop of the setting. In the books, some of the main characters are sidelined quite early. Some are important to begin with, and fade to almost nothing as the other characters take over. The central story is all about Paul Atredies, and everyone else orbits him and his manifest destiny. Trying to give equity to all the other characters is the wrong approach, because quite a few of them just don't have a lot of story to back them up. While these characters do have key moments, and are fleshed out in the book, I don't think a film has that luxury if it's going to be at the expense of the characters that drive the story.