There is no reason to fly short distance if you want to go from city center to city center. However, if you're already arriving or leaving on a long distance flight, the whole overhead of getting to/from/through the airport disappears and those 1.5 hours start making a difference. I think forcing companies to advertise more honest flight durations and prices could make a huge difference. If the airline tells you that…
And flights costing 29 EUR are simply a market (and policy) failure. In no reasonable sustainably operating economy would we ever have gotten into a situation of flights being cheaper than train trips.
That's a 1,160 miles / 1,870 km / ~2.75 hour flight (distance is as the crow flies). A train cannot compete with that. Not that a reasonable train itinerary between Lisbon and Rome exists.
For May 2021 [0], I'm seeing several roundtrip itineraries between Lisbon and Rome for USD$31 / €26 on Ryanair. I think the fact that such a low-priced flight can exist is actually a triumph of capitalism.