Maybe because the Beach Boys didn't have a lock on every song that came out in the sixties?

"Father?"
"Yes son?"
"I want to kill ye"
"Mother?"
"I want to &$F^&^U&*&C)&^C&%K" you, YEAH!!!!!"
~The End: The Doors

A large portion of the public saw Rock and Roll as "degenerate" "black" music -- comparatively, America was quite conservative going into the sixties. Segregation was still the norm across much of the country, especially the south. Rock and Roll was still new and early on, really was quite innocent when compared to more modern forms. Remember, this was a time when married TV couples were shown sleeping in separate beds, so even the slightest hint of sexuality offered in a song was morally wrong for a large portion of the population (Re: Let's Spend the Night Together: Rolling Stones). To have Elvis gyrating his hips on Ed Sullivan while performing offended a lot of people. The standards we hold today are quite more "liberal" than almost sixty years ago.

Well for one thing Rock & Roll didn't begin with the Beach Boys and while, as others here have rightly said, the Beach Boys never solely represented the complete spectrum of rock, they also appeared at a moment when rock music was made fairly tame compared to its predecessors.

To start, rock music has its musical roots in styles such as R&B, blues, jazz, and country. R&B basically meant music for African Americans and blues had strong connections to the black community, as did jazz. Country, while being much more of a 'white' style, was associated with the lower classes, meaning white trash. So rock is born from unholy marriages, so to speak, among musical styles from one undesirable element of society or another. What's more, rock had a nasty tendency of promoting amicability and mixing among black and white races. Many proto-rock and early rock shows attracted a mixed audience. At some of these shows there would be a string down the middle of the audience to keep black on one side and white on another. In the commotion of the show the string often came down. Think about the symbolism there.

Early black rock stars like Little Richard and Chuck Berry did loud, phenomenal things with their instruments and appealed to young, mixed race audiences by singing about poor boys in Louisiana ("Johnny B. Goode"), skipping school ("School Days"), or just upbeat songs that seemed to promote wild and rebellious behavior ("Tutti Frutti"). Notice here how it's not only black singers with mass appeal but they're singing about topics that aren't wholesome. One label famously tried to co-opt Little Richard's success by having an "acceptable" white singer, Pat Boone, cover "Tutti Frutti". It didn't negate the success or popularity of Little Richard, who famously said that the kids would buy Boone's record to leave out on their dresser while they hid his preferred version under the bed (from their parents).

I haven't talked about the white singers yet, people like Jerry Lee Lewis, Buddy Holly and the Crickets, or Elvis. Lewis played the piano so energetically he looked like he was having a seizure. In one TV appearance (couldn't find it on Youtube, sorry), he starts playing by standing so forcefully that the piano bench flies back off stage--but then you see it fly back on stage because the stage manager, furious, kicks it back at him (he misses).

Buddy Holly famously got one of his songs ("That'll be the Day") to the top of the R&B charts, which you'll remember is essentially "black" music. When they got booked at the historically black Apollo theater in NYC, the crowd nearly rioted when Holly took the stage because they, having heard the song only, assumed Holly and his band were black!

Elvis was (correctly) seen as a golden ticket by his label because he was a white man who could move and sound like those pesky (and popular) black rockers, giving him mainstream marketability. But even then he embodied a lot of the social degeneracy that rock and roll seemed to represent. He had lower class roots and still didn't behave in ways middle class audiences found acceptable. His early TV appearances used careful camera work to minimize showing his eccentric dancing.

The connection between rock and racial mixture and social degeneracy meant that it faced significant backlash in the socially and politically stringent 1950s. There were attempts to keep rock off the airwaves (or restricted to black radio stations) as well as vigorous public debates over the moral implications of the music. Within the music industry there were attempts to sterilize rock music by removing its immoral elements (think Pat Boone), exemplified best by Dick Clarks show American Bandstand. Look in that video how much space there is between couples, how nicely they dance, and how conservatively they're dressed.

A lot of this came to a head around 1959 and into the early '60s. To start, there was a large payola scandal that stripped DJ's of a lot of their autonomy in choosing what they played. A series of other events took many prominent rockers out of commission, temporarily or not. Chuck Berry was arrested and convicted for relations with a minor (though his sentence was reduced on appeal). Buddy Holly (along with other noteworthy musicians, died in a tragic plane crash. Jerry Lee Lewis was publicly ridiculed after it became known he married his cousin. Little Richard embraced his religious side and quit music to study theology. And Elvis got drafted into the Army. These things happened in such a short time span that there's an (unsubstantiated) conspiracy theory that many of them were orchestrated to try and kill Rock & Roll.

In the early 60s rock lost a lot of its initial controversy. The prevalence of tacky beach movies (several of which Elvis starred in once he got out of the military) and its associated guitar style, pioneered by Dick Dale, as well as the Beach Boys and the early Beatles, exemplify this trend toward "pop" rock. But, of course, the subversive roots of rock didn't totally fade away, as exemplified by the Beach Boys famously losing a lawsuit to Chuck Berry, who showed how "Surfin' U.S.A" essentially copied Berry's "Sweet Little Sixteen".