100 miles a week will keep you from turning into a slug. However, it's not that much so don't be surprised to not feel so good right now. As others have suggested, fatigue from the work day has something to do with how you feel, and you may be riding too hard. The nonvoluntary aspect of a commute and the fact that you're probably carrying junk makes it more tiring.

Stick with it. Your troubles will pass and this will eventually pay off big time. I'd say that if you wait a few more months, you'll gradually feel better and better. Eventually, you'll get totally addicted to it. You shouldn't be surprised if you're still improving in a year. It takes a long time to get in good condition.