I completely understand why BART does not allow pets onboard (assistance dogs aside). Not all pets are well behaved and not all owners are responsible. The last thing you want is to have dog poop add to the already plentiful stains on the floors and seats, or have someone's dog attack another passenger while in the train.
However, people still do bring small dogs on BART, sometimes not so small. I've seen it a few times. Little Yorkies or Chihuahuas mostly. On the most part the dogs are very well behaved aside from some occasional barking. I once even saw a little Golden Retriever puppy onboard....he was so scared and terrified of the loud sound of the train running through the tracks. I've seen people bring medium sized dogs in a crate covered by a towel.
Personally, I don't mind seeing people with their pets. Makes me happy. Keeps me entertained during my ride and distracts me from the other rude people on BART. I love animals. Dogs in particular because I'm the proud mom of the sweetest little pug in the world.
I could count so many positives to allowing dogs onboard but on the same note, I can think of a ton of negatives. Too many people just aren't the most responsible handlers of animals and it would just make BART an unpleasant experience for the rest of the passengers.
Would be nice though to take my little "king" to Embarcadero on a nice Saturday afternoon instead of battling weekend Bay Bridge traffic for an hour or more and be worn out and grouchy by the time we finally find parking!