Amtrak, BART or Drive in San Francisco?

If your hotel is near civic center, then I would drive to the hotel & pick your mom up at the airport. Since safety is your biggest concern, you will feel much better driving because the civic center area can get pretty bad late at night. Traffic to the airport & downtown are only crowded during commute hours, otherwise it should be tolerable. I would allow 1 hour travel time each direction to go to the airport & come back.