[nine_k]

Not only do take-offs spend large amounts of fuel; the fact of a landing and the servicing and refueling in the airport also cost the airlines.

Not having to land but instead having to carry some extra fuel while the engines work in their most efficient mode, and the air drag is low at a high altitude, should make airlines money. Else they won't try that :)

[schiffern]

Not just cost, but that limited airport "slot" represents (a slice of the) significant carbon emissions from building/operating the airport.

So even if you only care about carbon emissions, it can still make sense to skip the stop even if it causes slightly more total fuel burn.

[Ferret7446]

Semi-tangential, but this is why free markets are much more efficient than armchair experts.

Armchair experts won't correctly estimate all of these incidental costs nor the value of the saved time and overhead for everyone involved.