I think more accurately it's not crazy to think they might be doing something. I could equally be convinced if researchers crunched the numbers and concluded they might seem big but they're negligible on a global scale. In fact the same figure of "only 3%" of flights really have an effect" could easily have cut the other way.
A bit like how wind turbines look huge and numerous but are (as yet and for the foreseeable future) completely negligible on the scale of global wind power.
In fact plenty of times much closer to home, thinking "this very obvious thing must be having an effect" and failing to verify that it actually does has screwed me over repeatedly in everything from bug fixing to installing floorboards.