Even by Rolling Stone's standards that list doesn't make a lick of sense. It's very clear that the list is ranked reasonably randomly and that so many entries, and their placement, are obvious attempts to maintain relevance - like Kurt Cobain at #12, or how they group Lee Ranaldo and Thurston Moore together, as if they're saying "We wanted to put Sonic Youth in general on this list, but couldn't be bothered to actually have an opinion on which of their three guitar players is best" (the correct answer, by the way, is "Lee Ranaldo").
And the randomness of the rating is especially clear with someone like Mark Knopfler - I would say he is easily one of the top 3 guitar players of all time. As was pointed out, nearly everyone who plays guitar ends up playing as well as Keith Richards or Jimmy Page - they're riff players, they just happened to sometimes write really good riffs. Cobain rarely played solos and didn't even play many riffs; he just wrote good, simple songs with simple chord progressions, and lots of people do that and aren't on the list.
So, anyway, even people who read Rolling Stone for the music criticism are probably pretty confused about that list.