Good question. It's true that taxes on externalities are in some ways less objectionable than other types of taxes. One Bay Area libertarian thinker, Brian Holtz, writes (http://blog.knowinghumans.net/2006/09/libertarian-taxation-theory.html) that, "User fees are of course the ideal form of financing any product or service." But he qualifies this by saying, "However, governments should generally avoid them, because if the optimal amount of a product or service can be financed by voluntary transactions, then the government should probably not be involved in providing that product or service in the first place."
Not being an anarchist as I am, Brian does agree with what I presume is your position, writing, "Taxes on negative externalities (e.g. pollution) are a critical function of government." (Note however that gas itself isn't the negative externality; pollution is. If one person burns gas in a manner that emits less pollution than the manner in which someone else burns gas, it would be unfair to charge both of them the same gas tax.) However he adds that, "One of the best ways to tax a negative externality like pollution is to hold regular auctions for limited-duration emissions credits." This phrasing points to another issue with the current system: Rather than fluctuating according to market demand as auction prices would, a gas tax is an arbitrary, one-size-fits-all approach.
Furthermore, under a true libertarian approach, funds raised from such taxes or fees would not be used to pay for clean fuels research, mass transit, health care services, etc. – the money would instead go strictly to reimburse the victims of the negative externality (the individuals experiencing the negative effects of gas pollution). Right now, gas taxes neither go directly to the victims of the negative externality of gas-burning pollution, nor do they function as true user fees which use money raised strictly to provide services to the users who pay these taxes or fees. Instead, much of the coercively-obtained revenues cover unrelated government programs and spending, including paying for lots of overhead such as the inflated salaries, benefits, and pensions of people working in government (thus my use of the term "government greed").
Love & Liberty,
((( starchild )))