Why are hand-built wheels considered to be better than machine-built wheels?
I think a machine-built wheel can be just as good as a hand-built one, and vice-versa. This is probably an algorithmically solvable problem, so given fair conditions, whether human or machine - following the same rules for truing a wheel and tensioning the spokes - should achieve indistinguishable results.

There are three factors, though, that enter in the game:


There are some "tricks" to improve wheel quality that involve more than just turning the nipples. The most critical one, in my experience, is to properly bend the spokes around the point where they interlace one another, as recommended by Sheldon Brown here (look at the picture with the hammer, and the one where he uses a crankarm to bend the spokes).
Humans are better than machines to cope with the unexpected. In case of a malformed nipple or spoke, or any other surprise, a human can identify and correct a fault that a machine could let pass undetected.
The very REASON why a factory would choose to use a machine instead of a hand-building scheme has to do with cost-benefit of mass-production. It is not infrequent for this to go hand-in-hand with lower quality. So, a hand-built label would work as a "no-compromise" label for some products.


Hope this helps!