On a plane, you may have to get up extra early, or still lose half a day. Especially in Central/Eastern Europe, the prices aren't that high really. And, as GP already wrote, you save on one night in a hotel, which may offset the entire difference.
Also, there is the environment. If that were factored in properly in the prices (and that's being worked on), the train would be a lot cheaper.
I don't think you can really consider the environment here as there are too many variables to consider in a reliable model. E.g. its not clear that replacing that entire planes worth of peoples trips with another routing would even net a gain, if people might have to do more circuitous routing that take more time and distance, or take different modes of transit that aren't a fully electrified rail that goes end to end, e.g. a lightly filled bus that has a much lower per passenger mpg than an airplane.
I understand that some comparisons with realistic assumptions have been made. Notably, high-speed trains cause significantly more emissions than classical trains, but are still better than planes.
Also, there is the environment. If that were factored in properly in the prices (and that's being worked on), the train would be a lot cheaper.