Apple probably felt that they got burned by the last time they allowed Mac clones and ended up losing a lot of money. (I don't think that was the cloners' fault, but I wouldn't bother trying to explain that to Jobs.)
The cloners weren't growing the market, they were cannibalizing apple's own hardware sales. Jobs knew that, and canned them as soon as he got back in the big chair.
Another poster says the structure of the program prevented the cloners from providing a sufficiently varied product - that may be true too.
It kinda was the cloner's fault, but also the fault of Apple. Apple licensed the clones with the hopes that "apple-certified" clones to grow the market. I.e. figure out new and exciting ways to market macs to windows users, and demographics where it was failing (families, because the PowerPC performas sucked.)
However, Apple failed to certify more powerful clones (i.e. clones that were better/faster/cheaper than their big iron) on a reasonable timeframe. Cloners also contended that Apple was opening up the boxes to steal their trade secrets.
And the cheaper models -- that were often equal or superior to Apple's offerings, were a no-brainer for Apple's customers.
The long and the short of it is: Apple makes something like 30% profit off direct retail of their hardware system. Even on a mini that's pretty good. Compare that to $115 for the sale of OS X, and you realize they couldn't afford to keep the cloners around.
Not just faster Macs, but more frequent updates. And they were cheaper. I owned one. And a UMAX.
UMAX complained because their C500 model later served to be the exact hardware loadout of the Performa 6400 Tower. Apple let them do "research" on what chipsets could do what, and then took the result for use in their own hardware designs.
