I take the Hiawatha line from Milwaukee to Chicago pretty regularly and really enjoy it. It is a short run though, so I'm not sure how it compares to the OP of plane or train.
But I sure as hell know it beats driving downtown Chicago and paying for parking. I think that has a lot to do with my enjoyment of the train ride.
Edit: Oh yeah, and I've never been delayed (generally early arrivals) on that run and the fact that I can show up 5 minutes before the scheduled departure and still find a good seat is awesome.