Hi Amanda: If you take Bart to work, and you rent in SF, does that mean you work in Oakland? Anyways, the best advice in my opinion is your own "feeling" about walking in that neighborhood around the time you would be doing that if you would live there. Take a friend and ask for her / his input as well. I can tell you it is safe per haps, but my tolerance would be different from yours.
Try it out first is the way to go before making a commitment to buy. Have a Belgian pint at the Trappist before you go back to SF.