I was a tennybopper when "Freak Out" came out. (try downloading 'Hungry Freaks Daddy' to get a taste of it) I've heard alot of his stuff and I don't consider much of it very memorable. That album cover for 'Freak Out' was one of the most memorable in history, though. He was lauded as a musical genius probably because he was insufferably arrogant and condescending. Maybe because he believed in rehearsing and being sober while performing, in rock music that was unorthodox in the 60's. I remember a Monkees episode that he was a guest on, Michael Nesmith called him as a musical genius. I wouldn't say I hated Zappa but I didn't hear much from him to make me endorse the genius stuff. 'Willy the Pimp' was done with Captain Beefheart, he was really out there in the ozone.
I'd be astonished if it was true - That song was everything Zappa stood against. Zappa was an original booster of Alice Cooper, he produced their first two albums. Those albums stunk on ice, they were totally undisciplined. It wasn't until they linked up with Bob Ezrin and he taught them how to arrange and finish a composition that they became a good band. His genius didn't go very far in Cooper's case.
The only Zappa songs that I know and like are "Dancing Fool" (I love the line, "When I walks into the room, they all steps aside"), and of course, "Valley Girl".