I've recently started commuting also, came out of the car scheme at work, took the allowance/lump sum and have started riding.
Reasonably fit already, mine is 9.8 miles each way, which I do in anything between 29 & 33 minutes traffic/lights/weather dependant on mostly undulating country roads with a killer hill each end.
I would say its definately improved my fitness, i'm into week 7 now, having gone from trying every day, along with evening exercise on top (gym/squash etc) to realising right now thats not a good idea, so dropping the commute when playing squash.
Listen to your body, if you're tired and aching, take a day off, you will feel much better for it! Thats my best bit of advise.