If a bike makes you car free, it's a no brainer, commuting saves you lots of money, even if you roll on a big $$$$$ CF rig.
If it just means your car gets less miles put on it and you spend a lot on an expensive bike and lots of expensive fredly gear and you pay to have someone wrench on your bike, then yes, I would say that bike commuting costs you some, maybe even a lot. And it's worth every penny!!!
I bought my bike used and turn my own wrenches. I also have a bad habit of blowing off getting out of bed at 4:30 and end up driving. So, I would say that I'm somewhere close to break even. If I rode more often, I'd be a little ahead of the game.