Cars sitting in traffic don't have to waste energy. If all drivers drove hybrids, they would probably save money on total cost of ownership and wouldn't waste any gasoline while idling. Obviously we're not at that point yet, but if we're serious about sustainability we have to get there (and beyond there).

You can't improve conditions for existing transit riders without making transit more mainstream. You can't make transit more mainstream without making it less convenient to drive and changing the built environment, both in terms of density/land use mixture, and infrastructure for cleaner alternatives to the car.

To make that revolution happen, there might be a need to incur some short-run environmental costs. No worthwhile change is ever easy.

First, there the theory overcoming standing facts to become truth. There are countless peer-reviewed journal articles on the correlation between congestion and air quality, not solely from fuel consumption standpoint, which can alter with greater/worse fuel-efficiency, but primarily from idling engines. The author doesn't even acknowledge the latter; indeed, he completely dismisses an entire school of research in favor of some counter-intuitive theory purported as truth.

Then there's the total ignorance of social reality and the plight of those most apt to use public transit (which aren't the yuppies but rather the poorest citizens). From the article:

Time lost to traffic delays has an obvious cost—all those stalled commuters could be working at their desks or interacting with their children instead of fuming at other drivers—but perceptions of productivity are among the factors that commuters weigh when they consider where to live and how to travel to work.

Conduct a survey of existing MTA bus riders and I doubt "productivity" will even come out any where near the top of reasons of where they live and how they travel to work.

Ladies and Gentlemen, say hello to the future of alternative transportation!