You need a lot of infrastructure for trains (and a lot of it isn't even used all that much -- it's not like all rails have a train passing by every 5 minutes). You also can't get much use out of your rolling stock because the speeds are fairly slow. You also don't have the same flexibility as planes have regarding routes.

The upshot is that trains are a lot costlier than most believe think and most railway routes require state subsidies (with goods transport usually being an exception), whereas air traffic works so well it can be taxed heavily.

Air traffic is not taxed heavily compared to other modes of transport - on the contrary, it is very heavily subsidized (at least in Europe): Regional airports often strongly depend on state subsidies, airlines are exempt from petroleum taxes, flight tickets are VAT-exempt.

In Germany (and also e.g. Switzerland), long-distance trains are expected to run either at cost (or make a profit). Short-distance trains (regional transport) are usually subsidized.

Another factor is that building new rail lines requires eminent domain and acquiring land across multiple jurisdictions etc.

Why not invest in a vast 24/7 high frequency electric bus network instead of the big infrastructure costs of trains?