Chicago, I believe (correct me if I am wrong), has the largest transportation system outside of NYC. However, I personally think it's lacking.
There are two ways to get around: bus and train. And because there is no single comprehensive system like the NYC subway, it's really annoying that some areas are accessible only by train or only by bus (depending on where you live)... plus, it gets VERY crowded. You can literally sit on the bench and watch 4 buses go by that are too packed to let you in from 5:00 pm to 6:30 pm. They say this is because they're undergoing major renovations, which won't be done until next year (God willing)... but they keep halting construction due to lack of funding, etc.
Sorry, I totally ranted there...
I'll just say this: the people who say "public transportation is so convenient in Chicago" have obviously never owned a car. Though parking here is a real pain in the butt, and expensive as hell.
But that's the trade-off for living in a city full of interesting people and culture!!!