I think one of the biggest determinants of the fate of alt fuels will be the fate of hybrids. By that I mean that how people feel about hybrids in 5-10 years will determine how open people will be to the next new-fangled green technology. Explanation...

Hybrids are now on the road in significant numbers, and although many people are quite happy with them when new, we'll see what the people have to say about them when they have driven them in the real world for 100k miles and have to deal with them when they are old beaters. Those battery packs will eventually have to be replaced at significant cost to the owners, or else they will just be driving a weak, small-engined jalopy. Similarly, those spent battery packs are nasty little toxic waste dumps that someone will have to pay even more to dispose of. Hybrids can easily get a bad reputation for being far too expensive to be stuck with past a certain mileage, and that mileage point may be not much past the point where the hybrid drivetrain has just paid for itself in fuel cost savings. What if a decent number of owners had to pay $3k-$4k to replace the battery pack and dispose of the old one at 80k or 100k miles? That would be bad. And what if you let the battery pack die and drive the car into the ground, and STILL have to pay $500 or $1k to dispose of the pack?! That would suck, too! People who go stuck with those bills will likely develop a low opinion of hybrids.

If that eventuality comes to pass (and I think it will, at least to some extent), and the world starts pushing some new fuel/drivetrain technology to replace hybrids, people may be far less likely to accept the new technology after being ultimately burned by hybrids.

The other Big Problem facing any new fuel is building a new and duplicate distribution infrastructure. America has had gas cars and gas stations for a hundred years, and the gas distribution network has expanded organically with the population, development, and road construction (just like McDonalds ;-). Any new fuel system is not only going to need the cars to use it, but the distribution network to supply it - all across the country, and all at once. That will be very difficult and slow to develop, and will constrict the growth of the new technology. To illustrate the point, think of how rare diesel pumps were (away from the interstates) just 25 years ago. My parent's 1980 VW Dasher diesel came with a book listing all the gas stations all across the country that sold diesel! It was a tough fuel to find, and it was in use by hundreds of thousands of trucks across the country! How easy will it be to find a hydrogen station in 5 years? or even 10? It's not exactly an easy and safe substance to handle, either, especially when pressurized to 3000 psi. (Oh, and it takes more energy to make than it releases when used, but that of course could change over time)

Anyway, any alt-fuel will have to make economic sense to most people (not just a few of them) in order to be successful. If it costs twice as much to buy the vehicle and twice as much to run it, not enough people will want it for it to go anywhere.