Many matte boxes can hold additional items - like filters and french flags.
Sure, you can likely just plop a filter onto the actual lens itself... not quite so simple for camera-mounted flags. Which part you gonna duct-tape it onto?
Lens hood can be useful - just sayin', a matte box adds more versatility and choice.
Imo, the bigger the camera (and the more of a hassle to quickly move), the more benefit a matte box is.