Yes, it is a pity. On the other hand, Germany is only around 1000 km north to south, and most distances can be done in a few hours with conventional high speed trains. And it doesn't look like there'll be export opportunities for a Transrapid anytime soon to, say, the US, or China...
If you limit yourself to Germany you are correct. However the EU is a thing, and could be made a lot better if the countries started acting together more. Maglev from Italy to Finland with stops in Germany for example.
The entire world is full of difficult terrine. Either you quit making excuses and learn to deal with it, or you make excuses and make flying easier. I visit Europe about once every 20 years, so I'm not really in position to say what Europe should do.
Edit: I mean for the usage in Germany. It’s sadly a very political topic because lots of money went into this project.