Certainly, if you include the time you would have to spend exercising after your car commute (not to mention driving to the gym) to get the same level of exercise you get commuting by bicycle, you can express the commute time in minus numbers. If you look at it financially, the cost is also negative if you consider what driving the car costs you versus the bike. So biking is a negative activity!
Funny thing is I don't commute for the exercise ... I just like to ride and I don't like to drive, but it is nice when I go to my doctor and she says: "You know, you are in better shape than 99% of my patients your age."