The critical point is that while electricity comes from “dirty” sources currently, this is not necessarily how it will always be done. Using electric cars centralizes the pollution – rather than millions of individual exhaust systems releasing crap to the environment, they draw electricity from the grid and the exhaust is centralized at the power plant. It is much easier to control emissions at one source rather than many. Further, if technology advances it will be much easier to upgrade the power plant to make electricity from a cleaner means (solar for example). There would be no difference to the end-user (you and me) as we would still get our electricity, but the mechanism for creating it would be much cleaner. This is much more efficient than replacing millions of cars every time a technological advancement is made.
The downside is that whenever you centralize any system, you also centralize the power (control) associated with that system. You could hypothesize that one possibility of a centralized transportation system is that the one in control could shut off the power on a whim, Minority Report style.