It all depends on your baseline as to whether bicycle commuting saves money or costs money, or if it saves time or costs time.
I was a bus commuter for six years before I started cycling. Lemme tell you, using the bus with no car and no bike is really cheap. At least around here.
When I first made the decision to start cycling, I budgeted one year of bus passes, (12 @ $55/month, or $660) for nine months of cycling. I expected to spend $500 for a bike, lights, lock and helmet, reserving the rest for "incidentals", and figured I'd take the bus again through the winter.
Well, I blew through that $660 and more before I even discovered BikeForums, which is where I subsequently discovered things like studded snow tires, fenders, racks, panniers, realistic lights you can actually see by, clipless pedals, flat repair kits, tubes, tools, lubes, and the whole festival of other cycling accouterments.
Near as I can tell, that first year cycling cost me three years of bus passes. My current commuting bike alone cost three years of bus passes, before I started kitting it out. Its replacement cost is roughly 5½ years of bus passes--all before maintenance expenses.
And I don't regret a dime of it.
As for time, if I don't take the long loop to work, I come out ahead. The long loop comes out just about even with bus commuting time.
This is a really smart post and I agree with everything, especially the discovery of and bikeforums and bike-gear-porn.

For me the comparison isn't to a car but to using the El in Chicago. A monthly pass costs $86 dollars (I think - been using daily passes in the last 3 years for the rare times I take the train). I started riding seriously in late 2006 and in 2007-2008 spend over $3K on a new bike and assorted accessories. It will take about 34 months to recover those costs. These days I probably spend a couple hundred bucks a year for tuneups, tubes, etc. As a year round commuter I'm looking to turn a profit sometime in 2011-2012.
I have a wife and two small children. I could never get rid of the car so it's just a dumb comparison.