There is one other option that fits the same applications CNG does, but without the dirty trail. That option is electric vehicles.
Like CNG, electric vehicles would fit very well into municipal and industrial applications -- where vehicles return to a central station each day for refueling. The electricity for these vehicles could, of course, come from coal, oil, or gas but building the recharging and fleet infrastructures means that a door is open to a future powered by solar, wind, and other renewable energy sources.
In the end, CNG vehicles may be "cleaner" than conventional gas vehicles, but they are a short-term -- and possibly short-sighted -- alternative that excludes much more responsible solutions.