Food for thought. Does that matter? That is to say, society at large benefits from a transit rider. That transit rider has reduced congestion by not taking a private vehicle trip. He has also contributed less carbon emissions for his trip. In economics, we say there is a positive externality associated with mass transit. Thus, while it receives "subsidies," those subsidies may be offset by the (often intangible) benefits of the transit system being there.

But from an accounting perspective, no, fare box recovery ratios are never 100%.
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@All:
I agree that this is a problem. My issue with such reports about traffic congestion is that they only look at one part of the urban mobility system: roads. They are measuring the difference of the time on a congested road, against an ideal without congestion, and then assigning a value to that time. That is the cost. What about other modes?

That is to say, the urban mobility system is multimodal. People move on mass transit as well, which includes trains. Freight moves on trains as well. We understand that traffic delays cost the road-based transit system (i.e. buses). But the other mode (rail) is left out of the equation.

In larger cities, such as Chicago, there is an actual congestion and delay in rail. Trains are often delayed or not on time due to construction issues. Sometimes they are over-capacity (such as the Red-line after a Cubs game). Or pehaps the headways are not running as quickly as they could (maybe due to budget constraints). This is a delay cost to the commuter as well. In this case, the commuter is facing a longer headway, and perhaps a longer travel time and average speed, than he otherwise would if the system was given more capacity. Or perhaps if the rail system was improved with new infrastructure and technology that increases average speed. These differences in transit times, against an ideal, are costs just like a congested road against its ideal.

Looking at a urban mobility system-wide analysis would allow us to think of solutions that consider all parts of how people and stuff move. This report about traffic congestion tempts us towards the solution of "lets reduce traffic congestion by fixing and improving roads." Or perhaps improving transit, but only insamuch as it reduces congestion.

If we look at the cost of movement delays (which would include all modes), we can consider solutions that use a systems perspective. We would think of improving the train system not only because it reduces congestion but because it redcues transit travel times. Of course, it all is an intergrated system. We need to look at how people move, and their delays and times, in all modes. What matters is how long it takes for people (and stuff) to move from point to point. No matter which mode. Period.

See example from San Francisco: http://www.streetlinenetworks.com/site/index.php#