For the most part I agree with Zubrin. There has been too much hype about hydrogen fuel and there are many scientific, engineering, and policy issues that have to be worked out before a hydrogen economy could be implemented. One technology Zubrin ignores, however, is solid-state storage of hydrogen, for example, in the form of metal hydrides. Solid-state storage of hydrogen offers the possibility to solve the issues pertaining to the safe storage and transport of hydrogen fuel.
Of course, the technology is nowhere near adequate. Solid-state storage technologies are currently too slow to recharge, too expensive to produce, and too heavy to transport efficiently. However, these problems are not insurmountable as new research could improve the technologies to the point where they are commercially feasible. Although this is a big if, this is still an area of research which shows promise and deserves the funding its getting.
Hydrogen production, as noted by Zubrin, is the more fatal flaw of a hydrogen economy. However, some promising research is going on in this area, for example, in the biological production of hydrogen and in catalysts which use energy from the sun to produce hydrogen. If these technologies can be developed, they would offer cheap, environmentally-friendly means of producing hydrogen. Again, this is a big if.
So, I wouldn't come to the same conclusion as Zubrin that a hydrogen economy would not work. However, some major scientific breakthroughs are required before hydrogen would become a commercially-feasible and environmentally-helpful fuel. So, we should still be putting some research money into hydrogen technologies, we definitely shouldn't be putting all of our eggs in one basket.
On the issue of biofuels, Zubrin is a bit more optimistic than he should be. Currently, it is not clear whether the production of ethanol from corn is economically or environmentally advantageous since the energy needed to grow, transport, ferment, and distill the corn into ethanol may be more than the energy contained in the ethanol. Furthermore, growing corn and refining it into ethanol produces other types of pollution, for example, water pollution due to fertilizer use. On an "ethanol economy" scale, the US would not have enough suitable land to produce enough corn for fuel production while also keeping up with demands for food.
These problems would, however, be overcome by the development of "cellulosic ethanol" technologies, which convert cellulose (IIRC the most common biological material on the planet) into ethanol. Cellulosic ethanol would allow farmers to grow plants which are less expensive and demanding to grow (e.g. switchgrass) as well as obtain a higher yield of ethanol. While promising research is going on in this area, the technology is not near the point where it could be implemented yet. So, like hydrogen, biofuels (ethanol at least) require significant scientific breakthroughs before it can be a viable alternative to gasoline (albeit, cellulosic ethanol is definitely closer to reality than a hydrogen economy).