As I understand it, bike manufacturers buy their components, in bulk, at OEM prices from the component manufacturers. The parts they buy are shipped in bulk, without consumer-friendly packaging, instructions, etc. Their prices are nothing like the price that consumers purchase for parts.
As a consumer when you buy components they have been shipped in consumer-friendly packaging, get sent to wholesalers, who mark it up and send it to a retailer, who marks it up and sells it to you. So the price of assembling a bike piece-by-piece is typically much higher than buying a complete bike.
Some ways around this:
- buy used parts on eBay or elsewhere to build up your own bike
- buy a complete new bike from Bikesdirect.com, strip the parts, sell the frame on eBay
- find a dealer who is selling "gray market" OEM parts that have leaked into the retail market. I believe this is what some of the European websites like PBK do.
Seem thing with cars, by the way. If you had to build a car up from parts, purchasing each part separately from a dealer or parts store, the cost would far exceed what you can buy an entire car for.
BTW, last time I shopped for a build-your-own computer they were not any cheaper than buying a preassembled computer from Dell. The only advantage I could see is that you make sure you get name brand parts in every component.