Business-wise, Zappa was a machine in managing his music. In an article by Scott Harrison, he notes the fact that Zappa had two record labels (Bizarre and Straight Records managed with Herb Cohen), a mail-order company, a video company, and a music publishing firm - all of which was controlled by no one other than Zappa himself.
I've narrowed two main reasons why Zappa was an excellent businessman:
1.) Zappa knew how unsellable the Mother of Invention were to the general public. He will even admit to that in a quote:
...the top musical figures were the Beatles, Herman and the Hermits, the Byrds, Dave Clark and the Rolling Stones...the general trend of the music business was nice attractive young lads playing attractive, pleasant, listenable semi-cosmic pop music. The Mothers of Invention were unattractive old lads and we knew had an immediate merchandising problem. - 1972 Rob Partridge/Paul Phillips
He made it possible to still have his music available by having sound business plans and partners. Zappa actually studied the Byrds as a business model so he could launch his band in the most appropriate and successful way possible. He managed to become friends with the members of the Byrds and had them promote his works. Zappa did this quite often - using names and artists to somehow promote his stuff. It's a really clever strategy because it not only brings people to listen to his music who might not have otherwise, but he get's other people to do a big part the promotional work.
2.) Zappa was an absolute control-freak and needed to manage his music and business directly. It was his innate personality that would drive him to be a great business entrepreneur. In an interview, he explains why it was so necessary to be owners of a record label:
"...we [Cohen and Zappa] own our masters. I happen to like the idea of maintaining possession of the so-called works of art I'm involved in." - 1972 Rob Partridge/Paul Phillips
Whether it was writing his own music or owning his own business, Zappa always remained control of every situation. Control also was really important in keeping the integrity of his music. He was often battling with record companies because there was a mismanagement with not only his music, but with money. Zappa made sure that nothing was lost in translation.