I agree it's kind of silly to "rank" a classical guitarist, a jazz guitarist, a folk/bluegrass picker, and a rock guitarist on the same list.   It's like comparing Nureyev with Gregory Hines with Fred Astaire.

There are very few guitarists that I've heard play in a variety of genres, so I wouldn't be so bold as to rank most of them, but I do think some of these folks probably deserve as much recognition as some on that list, if not more:

Chet Atkins, Django Rheinhardt, Andres Segovia, John Williams, Doc Watson - Duh! I can't believe they were left off the list in favor of Joni Mitchell, Eddie Cochran, and Kurt Cobain.

Others I'd nominate for inclusion:

Pat Donohue - definitely - extremely versatile too
Charo - she's excellent
Paul Simon - very versatile
Paul Stookey - one of the best folk pickers I've ever heard
Roy Clark - pretty impressive pickin' there too
Christopher Parkening - another longhair, so I guess that doesn't count

And two women I'd nominate:
Nina Berger -- I wonder if the Rolling Stone folks even have a clue about Nina
Chrissy Hynde - Isn't she at least as good as some of those rock guys on the list?   Anyway, I'd rank her at least as high as Joni M

I've also been quite impressed with:
Jason Mraz
John Mayer
Brian Setzer
Roy Clark
Dan Fogelberg

not to mention quite a few studio musicians and jam buddies I've known, whose names are unknown to most of the general public.

The "best" and the "best known" are not the same thing.