Well it depends on your shooting style. A matte box really doesn't do much other than make flagging easy and convinient. The first obvious affect is the ability to easily get snappy blacks and higher contrast, but its all dependent on your lighting style. A soft backlight will tend to fall onto the lens. A small amount of light on the lens will make the blacks milky. too much and it will start to flare/ghost. If you are using pointy back light your going to get flare much easier, and you might find yourself moving a light rather than trying to flag the light off the lens.
Also when you introduce long movements into shots, a dolly for example, its much easier to pick up flares and much harder to use a flag-mounted stand to address them. With a matte box or french flag, you can cut light hitting the lens to practically only that light that is being emitted in frame (or reflected in frame) which does help control flares and contrast.
Of course the cheapest way to address light on lens is with a simple floor mounted flag. You often don't need much, just a C-stand, hollywood arm and a solid and your set. Its cheap, but its fixed (doesn't move with the lens for longer moves) and the weight and extra time it takes to set a flag might make a matte box better suited.
As far as filtering goes, with thread filters you can end up vignetting the image if you use too many, especially on wider lenses. A matte box will let you use 4x5 filters, or 6x6 etc. which will not vignette as the cover the entire feild of view, up to a few inches past the lens (thought the MB keeps them within the first inch of the forward opticle) also you get more options with grads and polarizers. Grads you can more accuratly place the grad, and polarizers can rotate mid shot to reduce reflections for an effect (off the top of my head theres a shot in Fast and the Furrious where its craning down to the guys car, and the filter rotates so you can see inside the glass...effects like that.
but if your broke. Blackwrap and a C-stand works just as well. Its convinience/cost question.
