Our personal standard has always been around the five hour mark when
deciding between train and plane
As long as you are one of the people who believes that Europe is just a few major cities separated by uninhabitable desert, the five hour rule might hold. I, however, find myself staying in a lot of small towns in this uninhabitable desert, and those towns are not usually close to airports, so by the time you take into account the time to get to an airport, the five hour rule doesn't work.
Case in point: three years ago, we went from St Goar, on the Rhein, to Pfronten-Ried, near Füssen. The closest usable airport to Pfronten was MUC, 3H21 away. Cologne/Bonn and Frankfurt were about equal distant from St Goar, 2H9, but it's a shorter flight (55 min) from FRA to MUC than from Bonn. Adding just the train and flight times, gets 6H25, and that doesn't include schedule mismatches or the required pre-board time (? 1 hr). The trip by train, St Goar to Bingen - EC to Ulm - Ulm to Kempten to Pfronten was only 6H21. Not only that, a SparPreis ticket for two today would be just under 60€, compared to over $100 per person just for the flight part.