You don't ride buses much do you? Of all the times I've ridden regular bus routes, there's only been one route where the bus being 90% empty would not be extremely atypical--and even then, that was only when I was picking up the bus during off-peak hours. More frequent have been the times where there being anything other than standing room available was the atypical situation.
If you're in an urban environment at least as densely packed as, say, San Jose, then the bus system is likely to have actually quite substantial ridership. By the time you get to the kinds of dense urban environments of the standard major US cities (NYC, Chicago, DC, Philly, Boston), I quite assure that the buses are routinely packed. The story might be different if we're talking about, say, Bismarck.
Furthermore, I should point out that if a bus is stopped "pil[ing] up traffic behind them", that's because it's letting passengers embark or disembark, which is a strong signal that the bus probably isn't 90% empty.