They should be. Artificially keeping jobs alive that are better, safer and cheaper performed by machines is bad for everyone in the long run, even the train drivers.
BART is already almost automated: the train drives itself. The "drivers" only close the door, and stop the train if something unexpected happens. Some other light rail systems around the world run with no drivers on board at all.
The progress of automation will certainly result in complex social issues, and the entire concept of employment may have to be rethought.
But keeping a small number of people pointlessly in their old jobs is not the right solution. Why should a few people receive $66-92k per year in welfare just because they used to drive a train, while other unemployed people and the homeless do not? It would be more fair to share the tax funds between all unemployed, regardless of whether it was due to a new automated train system or not.
Same reason for anyone in that situation: The sooner they learn/do something else, the sooner they can acquire a new useful skillset, instead of dragging on their now useless one. It's not like this is an intermediate problem and if we just subsidize them long enough, there'll suddenly be a need for train drivers again.