One of the main ways that Holden challenges society's values is in the way that he looks at the world. For him, nearly everything about the world is "phony," particularly the people in it. Everyone is a hypocrite, even the people that he at first appears to be loyal to like Mr. Antolini. Holden is unable to distinguish between what is genuine and what is phony, but in starting with the assumption that everything is phony, he suggests a different way of looking at things like society's values.
One of the smaller ways that he challenges society or societal values is the innocence he has that gets destroyed in various ways as he deals with the pimp and the hooker and the adults in his world.