Part of what makes debates about energy confusing to many is that the language of resource depletion allows one to make strong and accurate claims to justify widely divergent positions. Of course, we are running out of fossil fuels; they take millions of years to replace. Yes, we will never run out of fossil fuels; there will always be some amount that we will choose to leave in the ground because they are not worth extracting. You can logically say both or you can emphasize one. In any case, neither statement is helpful in getting to the core about why people care, and disagree, about energy, which has more to do with differences in values, appetite for risk, time horizons, as well as urgency of competing social priorities. Debates about energy poverty, climate change, and air pollution also have the requisite combinations of linguistic imprecision and real uncertainty to allow for strong conflicting claims.
The "are we running out?" framing distracts from two important points in Charles Mann's article. First, unconventional fossil fuels--fracking, tar sands, methane hydrates and several others--are growing in importance. Unconventionals comprise truly massive resources, but what makes them "unconventional" is that they are more dispersed than traditional fossil fuels. They are scattered around the world, they are difficult to reach, are mixed with other materials, and require much more processing to be useful. As a result they are almost invariably more expensive, more energy intensive, and more polluting than conventional fossil fuels. Adam Brandt at Stanford has probably done more than anyone in characterizing these resources.