I agree with everything you've said.  I guess people may see transportation as a specific enough sector (as opposed to "sales" or "income") that they feel it's appropriate those revenues go to something transportation-related.  A good start, though, would be putting more of that towards alternative modes of transportation (like transit) which have positive benefits (many of which Tierney mentioned) besides just mobility.

Fights over "diversions" of the gas tax began with the first diversions, to fund transit back in the 1970s, and continue with every single TEA revision. The auto-oil-pavers lobby still bitterly opposes shifting any funds from the gas tax -- their sacred "highway trust fund" -- to anything else, even other transportation-related uses.

The 4.6-cent (?) gas tax that made it into Clinton's 1993 deficit reduction package (as a replacement for proposals to do either a carbon or BTU tax) is the only federal gas tax that goes to the general budget.
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go to transportation.  However, it should be used to build more and better PUBLIC transportation, not more environmentally destructive roads.  Ideally, public transit should be free, paid for by gas taxes.

Also, while it's great to hear a libertarian (even a "semi" one) advocating more taxes, $.50/gallon is far too low.  $5/gallon would come a lot closer to meeting the goals outline above.