Film--even a whole trilogy of films--is a different medium from books. Books are in general much more tolerant of diversions that don't move the story forward. Bombadil was pretty much a diversion.
The films also had to deal with the fact that the LoTR books had a lot of material after the ring was destroyed--and that's not even counting all the material in the appendix of RoTK. Say whatever positive things you like about LoTR but the narrative structure of RoTK in particular is a bit of a mess.
I don't think it was "a mess" (just reread it this spring). Books support a lot more alternatives to structuring a story than most movies, with their tight time limits, want to explore.
That doesn't mean movies are better: in fact, movies are clearly more limited and worse, from the point of view of telling long, complicated stories. But people enjoy movies (me too), so... compromises.
The films also had to deal with the fact that the LoTR books had a lot of material after the ring was destroyed--and that's not even counting all the material in the appendix of RoTK. Say whatever positive things you like about LoTR but the narrative structure of RoTK in particular is a bit of a mess.