Here are some of the problems I had with the "The Real Price of Gasoline":
Road congestion is an interesting case of externality attribution: traffic is a huge cost generated by driving, and I'm willing to entertain the possibility that twenty or so years ago a gasoline tax might have been the most efficient way of addressing the problem. However, it is very clear that not all driving contributes to traffic equally (some roads are never clogged; some only during certain hours), and the technology these days is more than good enough to deal with it directly.
An even more subtle case is air pollution. Carbon dioxide is an inherent output of the burning of gasoline, so it makes sense to treat any and all costs of carbon dioxide as an externality. On the other hand, all of the other gasoline pollutants aren't inherent: they depend on either the car burning the gasoline (newer cars typically pollute less than old ones), or on the specific blend of gasoline being used (which varies from country to country and state to state depending on regulations). Now, maybe it turns out that the best way to address these variables is through a blanket gas tax, but I doubt it. I don't have a reference, but I'm sure someone has proposed a system in which your car gets a rating during its annual inspection, and that rating determines the gas tax you pay.
Anyway, the paper is just riddled with improper externality attribution: subsidized parking, roadway de-icing, etc., etc.
If gas was produced by a monopoly (call him Mr. OPEC), it's easy to see that granting Mr. OPEC a tax break wouldn't effect the price of gas at all: Mr. OPEC would just take the money and keep charging the same amount for gas. Similarly, if gas was sold in a perfectly competitive market, and the government decided to give a exploration subsidy to just one gasoline seller (call him Mr. Texaco), it's clear that again, Mr. Texaco just pockets the money and the price of gas is unchanged.
On the other hand, if the government gave a tax break to all the sellers in a perfectly competitive market, the price of gas would go down, as long as the size of the tax break that everyone got was at least roughly linked to the size of their market share.
As usual, the real world is somewhat in between: gas is produced by an oligopoly, and the U.S. government gives tax and program subsidies mostly to U.S. oil and gas sellers, in a way that is vaguely correlated with market share. My guess is that said subsidies are almost entirely ineffective in lowering the pump price of gas, but at the very least it is incorrect to count their full amount as an externality.