In my largest city, pop 47k, I have a good size bus and metro system covering most areas. The bus expenses are just over 800 at 115% funding with a profit of a little over 5000. The metro costs just over 5000 at 120 funding and brings in just over 4700. I also have a passenger harbor which does some business (bringing in tourists).
As for setup, I just tried to follow
@FlyingRoss's tips in his tutorial on mass transit.