I'm not commuting anymore, but when I used to, I would try to get some work done on the train, and if I did, go home earlier without feeling bad about it. We didn't track time at that job.

At my current company I can clock in via VPN and book time on whatever I'd work on, wherever I am. As long as I tell my superior that I won't be at the office, and as long as I don't have any meetings during that time, he's fine with it. I've committed to deadlines already, and if I don't meet them, he's in trouble, but so am I, so he trusts me.