Quite simply, by '69, America had come around. Hendrix moved to London in '66, a full year before the Counterculture -- and the music of their movement -- would really begin to take off. Until the late '60s, the most predominant forms of American rock music were Surf Rock and Garage Rock, both of which were highly regional.
For a case study, look no further than CCR -- a band with five #2 singles (the most by any band who never had a #1), who were vastly influential (and prolific) in the late sixties. They didn't release their first record until '67; until that they played as The Golliwoggs -- a pop-driven band that their label forced them to play as to cash in on the success of the British Invasion.
It's worth bearing in mind that CCR wasn't as "Counterculture" as, say, San-Francisco-Psychadelic-Rockers Jefferson Airplane or Quicksilver Messenger Service, but CCR definitely was one of the most well-known American bands by the end of the '60s.