The tricky part with hydrogen is the containment. You either need cryogenically cooled tanks to get it to a liquid state, or metal hydrides to store it chemically. Both have fairly poor energy density (by volume and mass). What's more, the fuels cells aren't cheap either, and some of the more efficient ones operate at very high temperatures.

For all it's faults hydrocarbon fuels are really good at storing energy that's easily extractable.