When Frank Zappa knew he hadn't got long to live, he gave a few really interesting interviews on how he thought his music would be remembered by future generations, if at all.
Almost twenty years after his death he was probably right (as he usually was) about the historical estimation of his music and personality by mainstream culture. Frank thought that he would mostly be remembered for his outspoken attitudes towards censorship, religion and politics, with his achievements in music being downplayed if not totally neglected by most folks.
If you mention Zappa's name to most people you will usually get a sort of "Oh yeah, he's that intense guy with the big mouth and mustache who plays that weird music...bit too avant garde for me". People 'in the know' of course, realize there is a helluva lot more to Mr Zappa than the stereotype churned out in tabloid newspapers or TV news slots.
He was an incredible composer of some of the most mesmerizing and genre smashing music to have come out of the USA since the birth of Jazz. Basically, Zappa had a Jazz sensibility and used this to deconstruct, explore, dissolve and fuse strands of music as seemingly diverse as Rock, Classical, Jazz and even Raga. The problem I think is partly his own fault: his outspoken political views and willingness to 'go public' on so many topics created a suspicion in many peoples eyes that he was merely a publicity seeker or loud mouth. I think this may have put many off even considering his artistic output for many years.
Frank Zappa reminds me a lot of William Burroughs. He has Burroughs' viscous intelligence, and amazing ability to mix genres and styles to create mind-blowing new landscapes of human consciousness. When Burroughs was first doing the 'cut-up's' with Bryon Gysin back in the 60's, they called themselves 'Les Voleurs' (the thieves) because of their ability to literally cut and paste others ideas into a broader and more colorful canvas.
Zappa was certainly unique, but he definitely stood on the shoulders of lots of other guys and gals to achieve his oeuvre. This is not a criticism, everybody has to do it to an extent in order to create. But, people like Burroughs and Zappa didn't just peddle other's ideas and pass them off as their own, they used them as paving stones to travel to other, vast, and far more intriguing worlds.
I think Zappa had a Beat spirit at heart, but not of the slightly wooly Kerouac/Ginsberg type, he was too acerbic and sharp for that, and had his feet planted firmly on the ground at all times, a lot like his counterpart in literature 'El Hombre Invisible'. Maybe, that's the trick though - Frank should have been a little more invisible to the mainstream media and let his music do the talking instead. He was an incredible guitar player.