I think manga is being looked down upon by many different groups for many different reasons. The non-artist population (haha, I cant' believe I just wrote that. Muggles anyone?), anyway, the non artist-population most likely doesn't recognize that the effort behind the manga-style is the same as for any art. Let's face it, most people thinks it's easier to draw any character in manga style then it is to make a still-life study. Considering all the one, two, three-step-by-step tutorials on the web it's not hard to see where this attitude may have originated.
I think this has a lot to do with why manga isn't respected as an art form: too many people criticizing it for its content, and not its quality.