Agreed, wheel building is something that people make a lot of money on, and perpetuating the myth that it is a black art helps them charge more. Most bike shop mechanics don't even know how to do it, believing that it is something a mere mortal could never accomplish.
An expert wheel builder can put together a great wheel in less than an hour. An inexperienced wheel builder who has a few basic tools, can follow instructions, and is willing to spend a few hours on it, can also build a great wheel. It won't happen as quickly, and you might scratch the rim a bit, but if you take your time and follow instructions carefully, you'll end up with good wheels, and for much cheaper than your snickering LBS mechanic could provide.
Personally I dislike any mechanics who laugh at their customers. If it really were a bad idea to build your own, they could explain why without laughing at you.
Good luck, go slow, and carry a spoke wrench and a spare spoke with you for a while, in case you need to retrue a bit if your wheel doesn't stay true (many wheels don't, in their first 100 miles or so, even pro built ones).
peace,
sam