The reason is that "factory built" refers to different wheels than are typically made by hand. Factory built wheels are usually proprietary rims and hubs that work together, usually with odd spokes that one doesn't normally find at the LBS. You pay a premium for exotica that may or may not be a nightmare to maintain: trying to replace a spoke, the rim, etc. Often these "boutique wheels" have very low spoke counts. What that means, and what Dan's article referred to, is that the forces required to keep the wheel true and under tension are spread over fewer spokes. When one breaks, the forces exerted from neighboring spokes will often make the rim go so out of true (picture a taco) that it won't pass between the brake pads: you can't ride it. These wheels may or may not be made by hand (there are machines that will lace, tension, and true a wheel).
On the other hand, hand built wheels are typically made from off-the-shelf components: standard hubs (Shimano, Campy, etc), standard rims (Mavic, etc.), and standard spokes. Repair is simple and readily available parts make for easy replacement when something goes (and no wheel lasts forever: ideally, the wheel will last until the rim wears out from brake pad wear!). Usually these wheels have "normal" spoke counts: 28, 32, or 36 spokes. When one goes, the wheel likely will go out of true only a little, and at most you'll need to open the brake caliper to provide clearance. Ride home, go to LBS, get a spoke the correct length, put it in yourself, bring it to correct tension so the wheel is true again, stress relieve the spoke, and you're done. "Hand built wheels" may or may not be made by hand, too: I think Colorado Cyclist uses a machine for much of the work, yet one pair of Ultegra hub/Open Pro wheels lasted me for many years before I gave them to my 200+lb friend, who also couldn't hurt or put them out of true.
Bike maintenance isn't rocket surgery. Read up on Park Tool's web site. Check out Sheldon Brown's (hallowed be his name) web site
for everything you need to know, from beginning stuff to the most advanced, in a very readable style. Buy Jobst Brandt's "The Bicycle Wheel" for everything you need to know about building and maintaining your wheels.
"Go yell at an M&M"