My alternative to bike commuting is mass transit, which only costs me $3.50 round trip. That mass transit money is untaxed, so it's really more like $2.50 out of my pocket.
Gym next to work for locker/shower is $55/month, so if I commute by bike full time, I just about pay for that each month (22 times at 2.50 each). So basically any bike related expense (tubes, tires, maintenance, capital cost) is out of pocket and costs me more.
However, still worth it to me because of the time saved. My commute takes the same amount of time whether it is by bike or mass transit. So I figure it saves me about an hour each night because I don't need to go out and get any other exercise. Plus bike commuting is much more pleasant than being sardined together with a few thousand other people on the train.