I always enjoy taking BART. I live down in the BA Peninsula, which is no slouch when it comes to things to do and places to go and scenic surroundings while you're there, but sometimes there are events that take you a little further from home.
Always a bus trip to get there, me being a long time public transit person, I am pretty good at knowing how to catch a bus from anywhere to anywhere.
Get to the BART station, and you must start being aware of your surroundings. I once was almost pushed out of the turnstile by a fare-jumper. Unfortunately crime can occur any time, and it does seem to be getting worse. Choose where to stand and wait, choose your seat carefully, and once you're seated you pretty much don't need to worry about being bothered.
One thing I always try to remember is to carry cotton balls in an Altoids tin for my ears, because it can get loud on the train. Almost right away, you're going through a tunnel, and the trip is under way. The car darkens a bit, and you can see your reflection in the window. Now is the time to check your hair.
A good long train ride always gives you time to get a lot of reading/writing done, and I always make sure to bring something to read and a journal. This is so pleasant I often think how nice it would be to just spend all day going back and forth on the train. If I was rich that would be one thing I'd do.