Commuting by bike is going to help your fitness much more than sitting on your ass driving. Unless you replace the time you would bike with something like swimming or other exercise.

I think biking to work will help you "tone up". Remember that biking uses different muscles than running. I find running to be a lot harder than biking. When I run, I don't stop, but with biking, I stop pedaling if I feel winded or need a break. Running doesn't quite work that way.

My commute is 8.5 miles each way. Doing that four days a week was beneficial, but adding in a 25-30 mile weekend ride helped improve my strength.