The "music business" hates Zappa for many reasons, but mostly for this one: Warner Bros were fucking every artist they represented. Zappa was the only one to sue them to get an accurate accounting of why he was apparently getting so little back financially from the relationship. He embarrassed WB so badly in court they had to say that their accounting records were damaged in a flood and the ones that survived later burned in a fire. You don't have to watch it, but here Steve Vai states that Zappa's advice to "own your publishing" literally saved him millions of dollars.
The "music business" portrays Zappa as a deranged, loud mouth, when he was anti-drug, Libertarian, brilliant and absolutely unafraid to speak the truth.
