Part of the problem is that externalities are difficult to measure and thus easy to "externalize" from accounting as well.
Another problem is the so-called demand heterogeneity for public goods - the more fragmented preferences for specific types of a public/collective good, the less likely public funding of that good due to the public opposition to it (cf. religious education). Similar argument can be raised for public transportation, which is used primarily by ethnic minorities and urban dwellers. Suburbanities are unlikely to benefit from it because of its marginal cost (they already must have a car, and switching to public transit poses additional cost - as opposed to urban folks who ride transit instead of buying a car). Ethnic prejudice is also a factor that contributes to this demand fragmentation.
The broader question is the visibility of public subsidies and wastefulness. Suburban development is heavily subsidized, but those subsidies go mainly to infrastructure (roads, utilities, tax breaks for developers) and thus less visible. Wastefulness is truly monumental and ubiquitous - e.g. strip malls being abandoned as new ones build next to them, it takes a lot of energy to maintain suburban homes and lawns surrounding them (for a comparison - my energy in in urban apartment is about $40/month comparing to about $250+ for a suburban home) . Yet the so-called public opinion turns its blind eye on its lavish wastefulness, but bemoans the cost of building an efficient rail system. This selective cost accounting also contributes to the lack of public funding for public transit.
wojtek