In a frame...
Financing. All manufacturing costs a lot of money to set up. Either you finance or pay someone else to do it (and they finance themselves or pay someone... you know the deal).
Materials. Carbon fiber is expensive. In many ways it's more expensive to work with (curing ovens, clean rooms, etc). Go out and research how much it would cost to buy some carbon fiber epoxy and cloth, and look into the various safety issues with working with the same. I abandoned a pet project after I realized it would cost $1000+ just to get started on what would really be a $100 item.
Time/Transport. It takes a while to get things from, say, the Far East to the US. Through customs. And time costs money when you're financing a lot of equipment. If you are financing a few million dollars in materials, equipment, and space, there's a cost per day or month that someone has to pay for.
R&D. Make a frame, ride it around, see what works, what doesn't, and try again. I'm lucky enough to have lived near Cannondale's headquarters for a long time. I got to test ride some weird stuff (elastic rear suspension road bike frame, and this was a serious ride looking for serious feedback) as well as see some interesting things a year or two before they appear in a catalog (like the newest iteration of the SuperSix). R&D takes time and labor. Both cost money.
Marketing. Logos, ads, etc cost money. Deciding who to sell to, what to make. It's why I bought a custom frame recently, instead of trying to fit a production frame - my body proportions are at the extreme of the bell curve and it doesn't make fiscal sense for a manufacturer to sell a frame that fits me well.
Sponsorship. You've probably seen the Velonews articles on how much gear the Slipstream/Garmin/Transitions/whatever team gets. That's all free, plus the manufacturers could be paying cash on top of that. The consumers pay for it all.
Copycat manufacturers. Even copy cat manufacturers have minimum production costs. They may not have the same cachet as the big names (Vuelta vs Zipp) but they still have to buy carbon fiber or pay shipping or whatever. And usually they have to buy whatever they're copying.
There's more but I have to help unload a truck.
cdr