A story on IndieWire alerted me to the fact that the commentary is now available as an audio download which you can listen to alongside a DVD and it is hard to see why he didn't like it. I heard the first 15 minutes and it's really amazing the amount of detail he goes into each scene and how specifically he understood all these roles, not just Ferris. He gives some truly succinct descriptions of the characters and the actors he chose to play those roles and why everyone fit the bill. There are some great trivial details too, like the fact that in the opening scene all four actors in the Bueller family, the mother/father and the son/daughter, were all actually dating and in love. Ferris' movie parents, in fact, got married after the film was completed!
This is one of my favorite films so, as a director, hearing the commentary is truly amazing. It's so clear Hughes knew exactly what he was doing with this film and, more surprisingly how comfortable he was with actors adding a lot of improv and material themselves. Hughes admits his favorite line in the moive ("not a lesson" after Ferris plays the clarinet) was made up by Matthew Broderick himself.