i have the opposite effect too. i'm more charged and amped up for the day when i ride in vs. days that i take the train. the ride in gets my system going and gets my body ready for the day ahead. when i take the train, i'm dragging all morning long trying to wake my brain up.

i can't imagine a 4.5 mile bike ride ever tiring me out to the point of exhaustion (my daily commute is 3x longer and it doesn't exhaust me). as others have said, you're probably just experiencing the effects of a cumulative and sustained lack of sleep.

it's also possible that you're not eating enough replacement calories, but 9 miles/day of bike riding isn't going to burn an inordinately large amount of calories. if you were going 40+ miles/day, that would be a bigger concern.