This one.

I was pretty frustrated recently when I got a flight for 20% less by clicking through from a Google Flights link than I did from searching directly on aircanada.com while logged in with my Aeroplan account. I know exactly why it's the way it is, but it's pretty discouraging to feel that loyal-customer behaviour like going directly to the airline instead of an aggregator is punished with a higher price.

Search processing also costs.

Usually it is done on GDS, which take their cut for each search. And those searches are frequently done on systems can remember 60s when they were created.

This right here. Searching costs nothing to run for them, except when the searcher finds a better deal.