I travel by train to Chicago because it takes about the same amount of time as driving, and I can do homework, read, and relax. The cost is higher than gas and tolls (parking is moot, as I park for free), but the benefit of being able to rest instead of driving balances that out, especially during the winter.
In the past, I traveled on the SWC every year because my then-boyfriend was afraid of flying, so it was the only way to see his family for the holidays. I also traveled on many LD routes I'd never been on before, and I was able to see some states that were new to me.
When I had the choice of plane or train, my choice depended on a few factors:
If my goal was to see the city at the endpoint and/or a person in that city, I flew so I'd have more time in that city/with that person. When you only have a week for vacation and you're dying to see some new city or a friend you haven't seen in five years, time is more important than scenery.
If my goal was to see the scenery along the route and/or experience a new train, I took Amtrak. In those cases, the train was the vacation.
If I was on a business trip, I flew since it saved time. The exception was a trip to Dallas; I'd never been on the Texas Eagle, and my company gave me permission to take the train as long as I covered the roomette charge.
I honestly enjoy flying. I love the hustle and bustle of airports. When I have enough time and I'm in a new airport, I wander around and check it out. I get through the TSA check pretty quickly, unless I'm stuck behind a bunch of idiots who can't figure out the belt/shoes/tray system.
Takeoff and landing are my favorite part. I always get a window seat so I can watch.
As far as "fresh air" is concerned, I just turn the nozzle so it points at my face. As a result, I never feel like it's stuffy. I think being near the window helps since it's colder and doesn't feel as confined. Plus, I'm 5'5", so the seat pitch isn't an issue. If the plane has screens, I keep it set to the map because I like to see where we are when I glance up from my book, just like people who watch maps on the train.
People claim you can't see anything from the plane, but I've seen many wonderful things. If it's cloudy, I feel like I'm in some awesome fantasy movie where we live on top of the clouds. I've see the Rockies in the U.S. and Canada. I've seen the salt flats in Utah. I've seen Chicago's skyscrapers looking super itty bitty, not to mention the beauty of Chicago's grid at night. On a flight from London, Ontario to Winnipeg, we flew across northern Michigan and I was able to pick out I-75, Houghton Lake, Sleeping Bear Dunes, and the Mackinac Bridge.
Yeah, clouds get boring after a few hours, but I could argue that some of the scenery from the train gets boring after a few hours too. I've seen enough junkyards, grain silos, and corn fields to last a lifetime.
So, honestly, it's a toss-up. I enjoy traveling, whether by train or plane, so it just comes down to time, money, and other circumstances.