For one, they're bulky and heavy. This makes them impractical for everyday automotive use as the technology currently stands. They're also expensive. At current pricing, they would have to be heavily subsidized by the government to be anywhere close to competitive with the internal combustion engine. Then there's fueling.
Most prototypes use either hydrogen or methanol to drive the cells.
Hydrogen is also highly explosive. Or choose methanol, which leads us to our fourth obstacle, infrastructure. A hundred years of filling stations won't disappear or convert overnight, no matter how many we bulldoze into strip malls. Until these problems are solved, we're unlikely to see regular production of fuel cell vehicles from any of the major players. Researchers estimate 10-20 years before fuel cell science catches up with industry needs.