- Trains are generally more comfortable
- Trains allow you to use your cell phone
- Trains can take you from city center to city center
- Trains don't have the same security requirements
- Trains are safer
- Trains are cheaper to operate (and so should actually be cheaper in the long run)
Planes are better over very long distances. But trains are better for regional travel.
However, where a train does make sense, is connecting other points along the route.
Air travel tends to be either hub-and-spoke between busy hubs and tiny spokes, or point-to-point between two busy points; rail travel, however, is always along a route that allows intermediate points to be served at similar levels-of-service as major destinations.
Whereas a Sacramento-Bakersfield journey would typically require at least one hop to SF or LA by air, train (and roads, for that matter) allow that journey to be taken without intervening hops, and serviced at a marginal cost, because the two lie along a route that a train would travel anyway. That ability to connect ancillary cities is where rail travel really shines, in ways that air travel can't currently mimic.