As far as I know, most of the noxious or carcinogenic chemicals in smoke, (cannabis or otherwise) are oil soluble. Which means that a bong is not actually doing much to protect you against chemical poisoning.
I think that the reason that bongs work to make smoking more palatable (and indeed, more healthy), has to do with the fact that they remove particulate matter from the smoke, that is, chunks of ash that go into the water and don't go back through the air and into the mouthpiece due to the force of gravity. While even the smallest of these pieces is a gigantic heterogenous piece of mixed vegetable matter on the molecular scale, they are still too small for the eye to detect. But even at such a small size, a bong works by seperating smoke by physical, not chemical means.
Of course, someone could build a bong carbed with alcohol or olive oil, but that would kind of defeat the purpose, wouldn't it?
Of course, this is all only theory, since I am not the world's largest expert on getting stoned or the physics of smoke.