Commuting can be a great workout. Like anything else, it depends on how you do it. If you noodle along at a slow pace, you aren't getting as much of a workout, but it's certainly better than driving a car to work. If you push the pace, I would argue that commuting can provide more of a workout than a typical recreational or group ride. That's because you are carrying much more weight and starting/stopping more frequently. When I started bike commuting, I was already in the habit of riding after work on the weekdays for exercise. So I initially didn't increase my total mileage by much, but went from riding about 20 miles/ride around the neighborhood (or in spin classes) after work to riding 10-12 miles/ride twice a day commuting. I saw no drop-off in my fitness from commuting. In fact, my fitness improved and I also lost weight -- particularly as I increased my commuting frequency and distance.

When commuting regularly, you also need to factor in recovery/tempo rides like you would for any training regime. If you ride hard every day, your performance is likely to decline rather than improve due to burnout.