After looking at the list again, while I would have Clapton higher, I'm not as offended and it's not at egregious as I originally thought.
For starters, as far as playing ability alone I think he's arguably only the 3rd best Yardbird behind Jimmy Page & Jeff Beck. Others that are better in that aspect are Hendrix, BB King, Buddy Guy, Prince and for my money Stevie Ray Vaughan. Robert Johnson & Chuck Berry were also trail blazers and have no issue with ranking them ahead of EC.
So strict guitar playing he's border line Top 10.
Now add this criteria:
We also tended to give an edge to artists who channeled whatever gifts god gave them into great songs and game changing albums, not just impressive playing.
For me that easily places artists like Joni Mitchell, Keith Richards & Neil Young ahead of Slow Hand and several more. I would have a hard time putting him in the Top 20. I would give an edge to Pete Townsend too who was ranked just behind Clapton at #37.
Does Clapton have even 1 game changing full album? 461 Ocean Boulevard maybe, but even as a fan I find myself really only listening to his Crossroads Box Set.
Just ahead of him in the 30s are Jerry Garcia, Brian May, Jack White & George Harrison. I really have zero problem with putting him behind all those dudes considering how influential & proficient they are respectively.