Businesses aren't going to hire extra staff to walk around telling 'concerned' customers the vapor they see coming from other customers isn't smoke. Easier and cheaper just to prohibit vaping. No amount of education will counteract the fact that vapor looks like smoke.
I would say this is the biggest factor for places that ban e cigs. People who see you vaping don't think oh look there's a vaper they think why is nobody putting a stop to that smoker over there? Perception is everything, even if people don't pull you up over it personally they're thinking someone should and any complaint to a manager of a place is reason enough to ban it.