I'm a second year and I take BART to school every single day.
I think it's reliable, safe, and cheaper.
You will of course run into the occasional strange smell or loud rider, but you get used to it.
I try not to take the BART home after 9:30 at night, but that is just a general rule I try to keep. I have taken it home later than that with no problems.
PM me if you have more questions. I can give you info on getting a clipper card and signing up with the school to get the student discount.