Aren't there studies that show the health benefits out weigh the dangers? I think the problem is more that it feels more dangerous and is, as a result, is often quite stressful.
That's the sort of comparison you can only make over the entire population. Looking at it from the perspective of an individual, it's a raw deal if my general fitness is improved but then two years later I get hit by a car and walk with a limp for the rest of my life.
I do bike commute and lived in Seattle for 7.5 years without a car.