Well, if fossil fuels/other "dirty" natural resources are used for generating the hydrogen, at least that's just one source of pollution. That can be more easily monitored and controlled than the millions of tailpipes out there now. Still, are the emissions from generating hydrogen-based power equal to, greater than, or less than the emissions involved in traditional power?
Furthermore, let's think about the emissions from burning hydrogen. It's only water, right? What do you do with millions of cars dripping water (I would think significant amounts of it) by the minute? Is our current road/highway system able to accomodate the runoff? Maybe I'm just being an idiot, but I'm not sure that this topic has been addressed much.
I'm all for finding alternate fuels. We can't burn dino oil forever. And although I do believe that the "greenies" are way out in left field, we aren't doing ourselves any favors by throwing smog into the atmosphere - and we're definitely doing some amount of damage.