I commute 25 miles per day, and overall I suppose I do save money even at the current low fuel price.

A few points relative to the OP's question:
1) My bike is super cheap compared to the car from the standpoint of maintenance and depreciation. I ride a $500 bike with an internal hub gear and it uses up chains and brake pads quite slowly.
2) Food. I actually don't see a huge variation in the amount I eat between riding and not riding. Even if I did, not riding to work should not really be seen as a great excuse to do zero exercise. If anything, you can count the commuting time as a huge savings because it allows you to do to things (comuting and working out) at the same time.