One of the most important issues for a commodity fuel for vehicles is that it be convenient and safe to transport. For quite a while LP Gas has been available as a cheaper car fuel. Even with increasing petrol prices it’s acceptance is well below 100% due to extra expense in storing the fuel (high pressure and more insulation are required), the more expensive technology in the engine to heat the fuel before injecting it into the engine, and the extreme difficulty in creating something as convenient as a Jerry Can for transporting LPG.
LPG is mostly comprised of Propane and Butane. Propane has the lower boiling point of -42.09C. Hydrogen however has a boiling point of -252.87C and therefore is much more difficult to store and transport.
The next problem with hydrogen as a fuel is that it has a very low density. The energy density per volume of liquid hydrogen is 10.1MJ/L while the energy density of petrol/gasoline is 34.6MJ/L. Not only is liquid hydrogen difficult to transport but the vessels you transport it in need to be 3.4 times the size! Having a 3.4x larger fuel tank in a car may not be a huge obstacle, but then there is the issue of trucks used to transport it to fuel stations which are already at maximum size so the truck fleet will need to be 3.4x larger with more people driving them etc.
Once these problems are solved there are a variety of safety issues. Hydrogen burns with an almost invisible flame, sustains a fire when at a concentration of between 4% and 75% of the air and ignites at a low temperature. For an explosion you need a concentration of between 18.3% and 59%. I won’t risk promoting foolish behaviour by describing details, but when younger I have performed experiments with ethanol and witnessed experiments with petrol that demonstrate that they are both far less dangerous. Page 22 of this document by the US Bureau of Transportation and Statistics gives more information about the fire risks posed by hydrogen fuel. Page 35 of the same document describes fuel cells as being 45% efficient and an internal combustion engine for methane gas as being 30% efficient thus giving overall efficiencies of 33% and 29.5% respectively. Of course using an Atkinson Cycle engine will give a significant efficiency benefit over an Otto Cycle engine and outweigh this. Also it should be noted that fuel cells tend to require expensive materials such as Platinum in their manufacture.
Hydrogen is promoted by clean-coal advocates (not that any form of coal power is clean) and the nuclear industry (electrolysis is one way of using a huge amount of electricity). But there are many better options for powering cars that are available right now at minimal cost, these include bio-Diesel, ethanol, and plug-in hybrid or electric vehicles.