Public transport is rather tricky to get working correctly, but if you do manage to get it that way, it will actually pay for itself (and make a nice profit too, in larger cities).
I think it's a bit too complex to discuss it in detail here, plus I'm not really an expert on the matter myself, but may I suggest the forums at
http://www.simcitycentral.net/ (although the DoD/DHS seem to have seized that one...) and
http://www.simtropolis.com/