The problem was software. Apple did not have the operating system to justify such a premium product. MacOS 9 was laughably dated, slow, and unstable, especially compared to Win2000 and WinXP, and OS X was years away from being ready.
The hardware writes a check that the software can't cash. Anyone would have been better with a PowerMac or a Win2k machine.
I own a Cube, and with OS X 10.4 installed it is a completely different machine. It boots faster than a modern Mac, and is light years ahead of aged Mac OS 9 and the early versions of OS X. It feels utterly modern, and takes full advantage of the tight integration between the hardware, LCD monitor, and USB peripherals.
Unfortunately for Apple, OS X 10.4 was released 4 years after the Cube was cancelled. I think that if Apple had OS X 10.4 ready in 2000, we would look back at the Cube in a different way.