It's beyond crazy that intra-EU flying ever became as cheap as it did. Truly an example of externalized costs.
The rough estimate of the amount of damage a tonne of CO2 released into the atmosphere causes is $196 (source: wikipedia).
A an economy class return flight from Munich to Barcelona (a typical night train distance) releases 0.45 tons of CO2 per passenger resulting in an additional cost of $88.2 (72.6€), 36.3€ per leg.
Every extra tonne of CO2 does cost $196+ (I’ve seen credible estimates as high as $400), but through offsetting you could verifiably ensure that more tonnes are avoided for far less.
As a crude analogy, if there is an oil spill (causing $$$ of damage), it would still be cost effective to plug the next oil spill for $.
Don’t get me wrong, the ideal scenario would be to not cause the first oil spill at all (in this crude analogy), but given that this seems impossible in our society, an offsetting tax on plane tickets could be a highly cost effective lever instead.
The simple matter is air travel is stupid convenient between any two points not directly connected or where the two points are far apart. Its faster by far on longer distances and scheduling is far more flexible.
... long way around
The cost structure that exist is because train transport suffers some serious disadvantages airlines are not stuck with. If you want to claim an externalized cost that may not be paid in full your only choice is fuel costs but understand only a little over half of rail in the EU is electric. Even with higher fuel taxes trains will be at a disadvantage as shown below.
Airline travel schedules, capacity, and routes, can be varied as needed. Trains are locked into sharing tracks, may have have service requirements, and as a result cannot vary their schedules by much if at all.
Airline travel can also add and drop destinations with ease. Trains obviously require connections to each point separately. Rail construction, maintenance, to include tracks and facilities, can rival or exceed air ports.
Trains have the additional cost of staffing requirements imposed by various governments along with capacity requirements that can be out of date.
Finally, while trains have the advantages of lower cost for the train and carriages adding routes is just terribly expensive and their environmental advantage is being eroded as other forms of ground transport move to electric and all bets are off once air can be done that way
Also interesting: Lufthansa is the company which probably good biggest single Corona-support, yet, in Germany.
All the new airports built well outside cities meant that low cost airlines could offer flights to (near) a major city fairly cheaply, which in turn pulled down prices for the entire market.
I think it's more likely to have been convenient for the politicians, who had incomes that fitted with taking weekend breaks to Paris or wherever, and good for their voters, on a holiday package to Greece.