In answer to the OP: In Europe, I definitely choose trains over flying. I have avoided flying intra-Europe even before all the extra security hassles. The reason: the European airlines' draconian restrictions on carry-on luggage.

On my last trip to Basel, Switzerland (from Japan), instead of changing planes somewhere and taking an intra-Europe flight to Basel, I just flew into FRA and then took the train from there to Basel. I then visited Bern for a day and then had to go to Paris, so I just took the TGV from Bern to Paris. Then returned to Japan direct from CDG.

Ironically, in Japan I have no trouble with domestic flying and even prefer flying over the shinkansen (bullet train). But anyone who has flown in Japan knows that Japan has the world's best air transport system. Tokyo's Haneda Airport, despite being the world's 4th busiest airport, is easier to use than, for example, Omaha! There are never any lines for check-in or security, boarding is a snap, flights are almost always on-time, and airline and airport employees are uniformly gracious, professional, and cheerful. It is an absolute paradise compared to the air transport system of the US.