The US DOT has approved transportation of methanol fuel cell cartridges in your baggage and carry-on luggage, according to one fuel-cell maker. If you're lucky enough to own a fuel-cell system, you'll definitely be able to fly with it come October, when the ruling goes into effect. But this ruling only allows you to carry the cells, not use them on the plane. I looked into it, and the FAA, a division of the DOT, is still apparently evaluating the fire hazards associated with in-flight operation.
Looking at the gamut of fuel cells (and not just the methanol ones covered in the ruling), the FAA appears to be afraid that the little chemical powerplants might explode. According to an FAA report from April 2: "Fuel sources [in fuel cells] range from highly flammable to relatively inert."
In addition to standard evaluation, the FAA says it will conduct "flammability tests...on existing fuel cartridges." And not just on individual units. From what I can tell of this report, somewhere the FAA will soon, or already has, set fire to bulk containers of fuel cells, and tried to ignite fuel cells that are in operation, connected to laptops or other electronics: