It seems like the article was being deliberately pessimistic. So I'm going to try and be deliberately optimistic
2) Why doesn't using nuclear power add up? Are we talking about costs here or pollution? Not acting will cost considerably more in the long run.
Transportation - we already have infrastructures for distributing gasses. Here at least natural gas is pumped into most homes. It would need some adapting but the system is already there.
4) Natural gas lights up easily, it's colourless and odourless. We still use it! We deal with this kind of thing with gas an oil anyway. In the UK we recently had a massive oil storage depot blow up in an accident. Hydrogen in the atmosphere? There is very little as it is so light, I would need to check but form what I did at uni I believe most of it would leave the atmosphere before reacting.
7) No one said it would be an easy walk in the park. We aren't looking for an overnight solution.
8) We aren't just scaling economies though, the technology is advancing all the time and becoming cheaper every year - not due to mass production. At one time computers were too expsenvive, using ridiculous components. But now they are all around us.
9) A gallon of hydrogen? You can't really talk about that. He means a gallon at standard room temperature and pressure. We already deal with compressed gasses all the time. And here they are talking about energy, they haven't considered efficiency. Most of the energy released by the cell fuel is used. Wheres a combustion engine is still very wasteful.
In reality the truth is somewhere in between. But I don't think this should be taken as disconcerting news at all. There were always going to be difficulties with it. But similar things would have been said about cars in the first place. How are you going to get petrol/gas (sorry English

) everywhere? All over America? Don't be silly...
We'll find a way