wwmiv's outline of a zonal fee, with its necessary and absurdly complex set of exemptions, had me gasping as I read it. But if I just take it in the spirit of "brainstorming" where there's no such thing as a bad idea, then I can calmly say "wwmiv, have you lost your mind?!?"

This would be a nightmare to implement and enforce.
We've always had a very simple solution for transportation funding, externalities, and incentives ---- excise taxes. Texas has an insanely low gas tax. If we'd been taxing at the levels that are commonplace in Europe, we'd have been able to afford adequate freeways and public transit. But our miserable political class looks upon the word "tax" with the same nuanced affection they have for mass murder.
We drive too much because we don't pay directly for negative externalities. Gas is too cheap, cars are too cheap, roads are too cheap. Buses are too expensive, rail is too expensive. In order to fix this, we have to internalized externalities and we've known for at least a century, at least implicitly, that the best way to do this is to increase the price of transactions that generate negative externalities by taxing them, and then subsidizing transactions that generate positive externalities.
Of course the establishing of taxes and subsidies is a nightmarishly complicated and politicized process as well, so I guess my final conclusion to this gloomy comment is that life is nightmarishly complex, and we're all going to die imminently. Enjoy!