You have asked a very interesting question, and this is usually what some of my (non-auto related) friends also ask. Keeping the answer precise, what you pay is the value of ultimate and finest hand-built manufacturing, which too use the best and costliest materials available on the Earth, the cars we are referring, have their engine manufactured using supreme technology. In fact, an entire team of experts is involved to manufacture the different parts of the vehicle, right from the upholstery to the engine. That rich and exclusive feel can be realized only if you personally check one. Also, No wonder, why the super-luxury-cars have a fixed wait-period of at least four to six months (Or maybe more than that, not ordered one yet!) because they are only made on order. The rest, well I guess, it is the several taxes etc. that add up to the cost, and after all, since only limited models of a particular car is sold, the carmaker has to include in that the expenses of their business/employees too.
+1 to 350Z's reply! Jayadev just search in youtube for the videos of some of the whole manufacturing process involved in making of some luxury cars. You will amazed to see the perfection and precision involved in their process. And of course taxes also plays a role!
There are some programmes in Discovery Turbo and NGC which telecast the whole manufacturing process of some of the finest cars in the world , try to see them. I think Zinam also has uploaded the making of Lambo in an exclusive thread here.