I don't want to put words into your mouth or say how you feel is wrong, but like I said, I felt the same for the longest time too.
Now my morning run is me time - I run where I want to run, I wave to people, I smile, I pet the random dog that runs up to me, I smell the fresh air, I sense the warmth of summer, the coolness of fall and the crispness of winter. I feel the sun on my back, the wind on my face. I can listen to music, I can listen to an audiobook - my mind is clear - think the most and remember the most when i'm out on my jog.
When I commuted to work, it was so mindless sometimes I forgot how I even got from point a to b. On the bus or the train or sitting in my car, I wasn't there with nature, I wasn't there in mind/body/spirit. I was kept busy by stuff I didn't really pay attention to because it was all a distraction from the commute that I lied to myself was what mattered as me time.
at 5:30 in the morning - there is a good chance you will see the stars set and the sunrise - the birds chirp. You run - you start feeling better, you feel healthier, you feel more alive. You get back home and that coffee tastes better, that shower feels better. YOur muscles ache less and less as you do it.
That commute - unless you happen to be lucky enough to be bush pilot flying the mountains of Alaska to get to work or a park ranger driving thorugh a national park to get to work usually doesn't offer what we take foregranted but forget what life should be about.
When I lived in PA i had to commute 1.5 hours each way and i too swore to myself how good that "me time" was...
figure 253 working days a year, in one year I spend 759 hours just getting back and forth to work - not including all the extra time, bad days, slow days or working late, or having to come in early or use my free time to study, answer alerts/pages or stay ahead of tech/services/requirements that is a lot of time. Really put into perspective when you realize 750 hours is essentially 19 weeks of man hours of worka year. I couldn't name a book, or learn anything new or remember a damn thing that happened during those commuting days - but i could remember how bad traffic was, what time every school got out and how often i ran across the same asshole on the way to work or home and what frequency life sucked because of holidays/events/activities going on.
i guess my point is, if you can enjoy it, by all means enjoy it, but don't do what i did and fool yourself into enjoying it without realizing you weren't getting out of it what you perceived you were.
Its kind of a shame we're good at convincing ourselves something like a jog, where we're alone in nature with mind, body and spirit is "bad" but in the hustle and bustle of senseless rush to get to work or get back home - we see that as a me time. (not saying this is how you feel, but how i perceive the quirks of our society)
Also, lets not forget, if you had a 10 minute commute to work your run may be at 7:30 instead of 5:30 or it could be at 5:30 pm instead of 5:30 a.m which may be more enjoyable for you. Or you could go fishing before/after work or just spend an hour at starbucks enjoying a coffee rather than sitting in traffic by choice.
The first year i stopped commuting i started going fishing at a small pond on my way to work. I'd just keep a collapsable rod in my car and some lures. I got good at catching large mouth bass and crappy and i got to see the bats, birds, fish, deer and that 45 minutes of fishing before work was the best healing for my spirit i could ever ask for. Thats mother fucking ME time right there!