Train vs Fly San Sebastian to Madrid

The scenery is quite good through the Basque Country; beyond that I do not know. The carbon footprint is much smaller, too, which is a clear 'pro' of the train, and the train station in San Sebastián is conveniently located; quite walkable from most of the city centre.
All of the above makes me lean towards the train. Flying will save you at most 1-1.5 hours, which should not be critical in the context of a vacation.

Nine years ago, in October, we were heading the opposite direction - Madrid to Basque country. We took a 5 hour, early morning train from Madrid to Bilbao. We later rented a car, and had it for driving around San Sebastián, and points farther east. I’m not sure we’d even considered flying, and the train seemed to be our best option - maybe price. That was a looong 5 hour train journey, especially early in the morning. It was a rainy time of year, and I don’t recall the scenery being particularly stunning, not exactly postcard views outside the train windows, mile after mile.

Scenery on the mountain roads south of San Sebastián was beautiful. If price is about the same, and arrival time of day is about the same, it sounds like flying would give you more time in San Sebastián, before your departure flight.

When you add the airport faff and getting to and from airports the time difference is not that big so you won't save a lot of time by flying.

The scenery is nice, but not stunning. And trains are also in general a more relaxing way to travel and you can use the time to read, watch a movie etc. And as mentioned, the carbon footprint of a train trip is a fraction of flying. So for me, it would be the train.

Many thanks to all. We are now leaning towards taking the train.