Autos have a death rate of about 1.4 deaths per 100 million passenger miles (not sure if this includes pedestrian deaths due to cars).
Caltrain carries about 180 million passenger miles per year.
Between 1992 and 2007, Caltrain has had 167 track fatalities (this is excluding 2008 which is looking like it could be the deadliest year in Caltrain's history).
167 deaths / 16 years / 180M passenger miles/year = 5.8 deaths per 100 million passenger miles.
If you exclude suicides, it's still 67 deaths, 2.3 deaths per 100 million passenger miles.
Be careful around those tracks...