And even so, no one had awakened the fruit in 800 years. What were the chances some upstart kid was going to? People underestimating Luffy has been part of the story since the East Blue. And after Alabasta, where he really made a name for himself, he quite literally vanished off the map, fought Foxy and had a run-in with Aokiji but managed to win him over enough to be spared, dealt with Lucci where Garp then went after him but no one expected the Sunny to fucking fly, got lost in the Florian Triangle where Kuma was sent to murder him but that didn't pan out, then the Straw Hats all got separated and after some solo shenanigans, Luffy was on a random-ass island for two years. After the timeskip he went under the ocean, just so happened to make a pit stop to Punk Hazard that no one could've predicted, ended up in Doflamingo's territory where Fujitora should've taken him out but didn't, then he was on a phantom island and in the middle of two Emperor territories in a row before the Elders finally had him pinned down at Egghead.
Considering so many of these arcs take place within a few days...the World Government just had no fucking time to take him out in a majority of cases.