Punk is one of the few genres of rock that created its own unique subculture which has spanned generations and that still exists today. Punk was a cultural answer to big-stadium corporate rock bands, like The Who, who some felt, alienated their audiences. Punk's musical form is a symbol of that counter-culture - basic three-cord theory combined with direct anti-establishment lyrical themes. In otherwords, they stripped music to its raw core to strike at the corporate power base that tried to take music away from its intended owners - the musicians and the audience.
The Sex Pistols - being one of the more "popular" punk bands (kind of funny to say that) - absolutely deserves recognition, but it is ironic that they would be in the R&R HOF given Punk's roots and purpose. Therefore, it wasn't simply anti-establishment for them to stiff the HOF, rather they were consistant with what Punk is about. Even if you hate Punk (I am not a huge fan from a musical perspective) the music's role in the evolution of music is almost unmatched since blues and jazz.