Motherboards are cheap almost solely because of scale - they're sold by the tens of thousands, if not hundreds of thousands. They're also sold at a much lower margin (I would imagine). They also benefit from having an in-house production chain, e.g if you're Foxconn you have an entire city working just for you. As a hobbyist you need to pay someone else to make things for you (and pay their salaries +overheads too).

My comment about resistors was that most assembly houses will give you certain components for free because they're an insignificant fraction of the price. Also because almost every digital PCB will use e.g 0.1uF capacitors, they can buy enormous quantities. If you look at the link below you see that most of the cost is in the few specialised parts like the North/southbridge, sound card and connectors.

Here's a teardown and BOM analysis for a motherboard: http://electronics360.globalspec.com/article/3280/asus-p5kpl... . Note the BOM cost is essentially the sale price.

This is partly why Apple's stuff costs so much, because they actually price their devices reasonably (from a business sense). Everyone else works on razor thin margins to give you the illusion that hardware is cheap.