More energy is put into manufacturing flashlight batteries than what the batteries can produce. So does that make flashlight batteries a bad deal?
Think about it for a minute and you will understand why you can't say that energy in vs. energy out equation is the only way to measure the value of a potential source. If we can convert wind, solar, tidal, biomass or nuclear energy, or a combination of them, into a potable fuel source, the economics could very well make a lot of sense.
I don't know if it will happen, but I do know for a fact that fuel cell technology has reached the stage were it makes a lot of sense to start serious R&D of the hydrogen fuel cycle.
The scale of flashlight batteries is a bit different from that of automobiles. The two can hardly be compared.
Do you run your car on flashight batteries? You could technically.