I didn't read all of the Zubrin article, but I saw a seminar a few years ago by a professor from Wisconsin-Madison with a second-law analysis of Hydrogen production that basically said the same thing: you can't get out the energy that you put in. He included the transportation costs, if we were to pipe hydrogen gas in the same way we pipe natural gas, the costs would increase even more, because the energy density is so small. He also said that the best way to make hydrogen into a fuel source is to connect it with carbon molecules and make long hydrocarbon chains.

Did he talk about the carbon emissions associated with that?

Naw, I'm pretty sure it was pure-thermodynamics; no environmental speculation.

And, anyway, if you wait long enough the carbon and hydrogens put themselves together for you. The emissions only come about when you take them back apart. :)