Hydrogen is an energy *vector*, not an energy source. The energy must come from somewhere - natural gas usually - and, as TFA's author points out, the efficiency of the entire chain from energy source to the wheels is quite insanely bad.
Vectors are an important part of the overall equation. Different regions of the world have different viabilities of energy production. Some areas have lots of wind, some lots of light, some with rivers that offer a great opportunity to dam and harness the energy. Iceland currently generates nearly 100% of their electricity from renewable energy (75% hydro, 25% geothermal). It might make sense for Iceland to use their natural energy production assets to store energy in a 'vector' and export it. If that energy can go to areas where energy production is more difficult or comes at a higher environmental cost, it might be worth the efficiency loss.
This, however, doesn't mean that there aren't better options than hydrogen as the transport vector.