A few points.

1. A <1% risk of loss, if catastrophic (e.g. thrown off the platform into an oncoming train), is unacceptable to bear, when there exist alternatives.

1b. Of course, people get in car accidents all the time. However, rightly or wrongly, people feel more in control when they're driving compared to when they're using public transit (or similarly, taking a commercial flight), which makes them feel better about it. And there is some element of sense here: accidents do not occur evenly among the population, because some drivers are better and more alert than others.

2. If you're traveling with small children, the various (however rare it may be) unpleasantries of NYC public transit become an order of magnitude more unpleasant.

3. There certainly is an element of Stockholm syndrome among NYC transit users, in that other very large cities around the world with ridership comparable to NYC have very little antisocial dysfunction, but in NYC it often gets waved away as "part and parcel of living in a big city".