They were tired of not being able to control the presentation of their material to the masses. By not controlling the means of media presentation, artists leave their destiny in other people's hands. For example, an artist may wanna ignite passion and strike an emotional chord with his music while the radio station wants to make dollars and remain number 1 in the market. The artist in this case may find himself continuously frustrated.
Commercial radio exists to satisfy the tastes and needs of it's targeted listening audience.
On the other side, a rap artist should not tailor himself or his music for radio. This is different then making a clean version of a song. In short they start to play the radio game in which case the balance of power gets handed over to the commercial stations. The days of us having to beg a middle man for us as artists to have access to our own communities is over.