As a frequent MUC-TXL traveler, I’d say that now the train connection is finally en par with flying. It’s has now become a real alternative.

The hidden times you mentioned depend heavily on where you live and what your destination is. Going to the train station can be painful in the first place.

Another thing to consider: I regularly feel sick when I work on trains not so when flying. That’s why I prefer a long plane flight to a train ride.