You don't have as much security concerns, you have far more legroom, and the constant ability to walk around the cabin at all times (often to the dining car where you can get overpriced beer / light meals, but... better than nothing at all). Hour-for-hour, a train ride is far more comfortable than a plane ride.
However, once we start looking at 4-hour or 8-hour train rides, the idea of a 2-hour or 3-hour plane ride just starts to make more sense, even with 30+ minutes of security + many minutes of "Taxi'ing on the runway" involved. Flying at 500mph just makes more sense than train rides at 50mph.
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An exception is when the ride itself is part of the journey: if you want to see the entire countryside, the train is superior.
Planes fly over everything and are often high up in the clouds, so you don't get to see the whole ground.