Engineering hydrogen cells is tricky – to store a decent amount of it, you have to store it at really high pressure, and high-pressure flammable explosive gas is a bit of a safety nightmare.
If you’re designing that, you have to be able to explain why no head-on, rear-end or T-bone collision could possibly rupture your hydrogen storage and start a fire, and that has proven difficult. Even once you had perfect cars, you’d have to develop safe hydrogen tanks and safe fueling station infrastructure and build it nationwide.
We’ve already got electrical-power infrastructure in every home; it’s tough to compete with that.
*Edit: Really fast math tells me that a gallon of gasoline is 33 moles of octane, which releases 181 megajoules of energy when it turns. A mole of hydrogen burns for (being generous and assuming liquid water as the product) 285.8 kilojoules, so it takes 633 moles of hydrogen to match a gallon of gasoline. 633 moles of hydrogen at ambient conditions would be a 15.7m^3 cloud, so a ball about ten feet across. If you want to get that down to the size of a fuel tank, you need a pressure of about 200 atmospheres, or around 3000 pounds per square inch. Quick reminder, this isn’t replacing a tank of gasoline; this is replacing a gallon of gasoline. For flammable gas you probably design that tank for at least 12,000 psi. Now you get to calculate how heavy that tank is, and see what it’s doing to your car’s performance and efficiency, and you’re probably not going to like the answers. :)*
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