Well I think you have to look at an entire career comprehensively. I don't think the list is based on skill alone or showmanship or albums sold. I think 1-10 are pretty much a representation of their respective careers. Say what you will about Eric Clapton's guitar playing (there are better players), but as a performer, songwriter, guitar player - he def deserves to be in the top 10. And for those less than stellar players, the Keith Richards and Kurt Cobains, those guys changed the face of the genre. Keith Richards wrote some amazing songs and the Rolling Stones would not have been the same without him. Cobain wasn't that great of a guitar player, but his music encapsulated an entire generation and altered the face of rock and roll. So I don't look at this list as "This guy is ranked higher so he must be better than all the rest," but rather as a recognition of a career and influence on other great guitarists and rock and roll itself.
On a side note, Derek Trucks being at 17? or somewhere around there is ridiculous. He's a good guitarist, but he grew up with a famous dad in the music business with one of the greatest bands (Allman Brothers) and he's married to a very talented musician (Susan Tedeschi) that happens to front his band. He might be good, but he probably wouldn't have made my top 100.