Where I'm coming from:
I have a 4 mile commute. I am not a bike-commuter, as I usually drive my car. I have ridden my bike numerous times though and I enjoy it a lot. No matter what, my wife and I each have to have our own car to enable the flexibility of picking up our daughter at day-care.
So, I am going to own a bicycle and a car no matter how I choose to get to work. They are both sunk costs. The purchase cost of the bike (or car) shouldn't be counted towards your cost of commute if you are going to own them anyway (such as in my case). From there, I figure I am only saving money by riding my bike. Saving gas and car maintenance puts a few pennies back in my pocket every time I ride the bike. Like others have mentioned, the intangibles are priceless (I feel good not contributing to the horrible traffic in the DC area), so we can leave those out.
I won't count the cost of my bike or anything else I have put on it so far (lights, computer, air pump, etc.) against the cost of my commute because I would own them either way. Now I am thinking about spending about $100 for a rack and some bags since the backpack is annoying. That I will count towards the cost of commuting since I wouldn't own them otherwise, but that is negligible compared to the numerous years I should be able to use them. A few tanks of gas will easily cover that.
With all this said, I think I would save less than $400/year if I commuted EVERY DAY, which I am not going to do in the worst weather. So, I agree that in most cases, you can't sustain bike commuting on the $$ alone - it has be something you want to do for many reasons. But, I think it should be noted that no matter what, bike commuting is cheaper (except for the guy whose company hooks employees with train passes. You really should hit your company up for some sort of subsidy).