They never came around to his licensing model - that's why he killed the clones. It could have gone differently.
From what I've read, Steve Jobs did not want to get into the software licensing business like Microsoft. He has favored a more hardware-centered model, and the clone manufacturers were direct competitors in terms of hardware. In fact, the clone makers were beating Apple on price and in some cases performance too.
Had Apple continued with the clone experiment, it's likely that Apple would have been run out of their own hardware market - which, at the time, would have probably put them out of business.