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Hydrogen is most produced from natural gas. The extraction of hydrogen pumps tons of CO2 and other green house gases into the atmosphere. While it might be an alternative for gasoline it is not a clean one.
Bio fuels are terribly inefficient. It takes a gallon of fuel to produce 1.2 gallons of bio fuel.
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Those are the kinds of problems with production methods I was talking about. None of them are insurmountable; the technology just isn't mature yet because there hasn't been much public will to develop it. We also have ways of producing H2 from water and electricity which can be produced from renewable sources. The trouble with that though is it's slow. Last I heard the production of biofuel was worse than 1:1. You have to keep in mind that we've put almost no effort into optimizing either process though so we shouldn't write them off. We have to judge the alternatives based on their potential, not where they're at now. Keep in mind when oil refining first started that people though gasoline had no potential and literally threw it out.