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Nornagest comments on How can I spend money to improve my life? - Less Wrong
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Mile for mile, biking is significantly more dangerous than taking a car (as is walking), though not as dangerous as riding a motorcycle. (See here, or here if you're willing to tolerate older data and worse formatting.) You're trading off for physical fitness, though, and the life expectancy gained from increased fitness -- especially if expressed in terms of QALYs -- generally outweighs that lost from increased accident risk.
This undoubtedly varies by location but I haven't been able to find any good data on how. The waters are also muddied a bit by the fact that bike advocacy organizations like to promulgate the life expectancy data without the accident data -- not that I can really blame them, statistical literacy being what it is.
The one study I've seen that looks at the net health effect of cycling came to the conclusion that cycling is a net benefit. Loads of bicycling advocates promote this to suggest that cycling is in general a net benefit for you health. Unfortunately for North Americans, the data in the study came from Europe. Cycling is much safer in Europe. I am not aware of any analysis using data from North America, and I'm unsure whether such an analysis would come to the same conclusion.
With this being said, I ride a bike for transportation. I read studies on safety and actively try to minimize my risk. This includes minimizing my mileage, as the risk is per unit distance. So far, so good. I haven't been in a real crash yet in 4 years of commuter cycling, though I've had plenty of close calls. Worst I can say is that I did once hit a pothole and fall over, but there were no lasting effects.
SF in particular has been working hard on bike infrastructure improvements that should help with safety. Especially if your commute involves Folsom St.