This is one of the questions I thought of as well when I started out commuting. During the process I actually forgot about it. I think I'll write down the costs of a whole year of mass transit commuting, and compare that to what I've actually spent at the end of the year.

Right now I don't really care about the costs, as I like cycling far more than being stuffed into a train or subway with thousands of others. It makes me feel free.
I get to listen to my own music, enjoy the birds waking up, watching people admire my speed when I go by, see beautiful girls whizz by in the opposite direction... I love every aspect of commuting. The money has just become a nice side aspect, since I trust that I'm actually saving a penny.