I'd say that the biggest cost that goes into a frame is R&D. Prototyping is one of the biggest sunk costs in industries of all kinds (something on the magnitude of tens of billions of dollars are spent each year by Fortune 500 companies). Manufacturing techniques are pretty cheap, relatively. Society has been at it for a while and have it pretty much down pat.

However, that doesn't mean that the biggest cost that goes into making a finished product is the biggest cost in the overall price of it. Cyclists are suckers for anything that says "lightweight" and/or "aerodynamic," so marketing bikes and, like rpenmanparker said, value pricing are probably the reasons for higher prices. I'd venture to guess that in order to make a frame that retails for $3000, it costs less than $1000 for manufacturing, marketing, and distribution of R&D costs. But that's just a guess.