I've said it before and I'll say it again:
It's because it's what the market will bear.
We have no idea the R&D costs or the production costs into making such a lens--unless those people here who have speculated are, in fact, optical engineers involved in the development and mass production of such lenses, in which case I'll stand corrected. We don't know if it costs a team of fifty engineers working around the clock for two years to squeeze out that extra two stops, or one engineer made it when s/he got around to it after all the other lenses got equipped with VR. We can guess by reading between the lines in Nikon's financial statements, but we don't know.
And how are such lenses produced? Hand-made? I doubt it, but it's possible. I've heard anecdotally that Zeiss lenses are individually hand made and tuned, and it's that attention to detail that is reflected in their cost.
So while @Stan Roger's answer provides some potential optical engineering challenges that have to be overcome for such a lens, we on the outside of the production facilities have no idea if those problems were the major ones, or if solving them warrants the price. Other answers could also include interesting discussions about the exchange rates of yen to dollars, marketing projections, or other such topics. All guesswork.
Nikon feels that the lens should cost this much. I, for one, think that they're overpriced. If enough potential customers feel this way, look for price decreases in the coming months/years. If the lenses sell at their current price, then Nikon priced them accordingly (and I'll be looking for another 50mm f/1.4 equivalent for my d300).
EDIT: Not to say "I told you so", but, I told you so.
Samyang just announced a 35mm 1.4 full frame lens that will retail for €379, a fraction of the Nikkor's price but with similar specs. Will it be better or worse? I'll wait until lens reviews come out. But will it be that much worse as to justify quadrupling the price for the name of Nikon? All discussions about the cost of the technology that goes into the lens, etc, are all justifications given by sales and marketing. In the final analysis, if you have a competitor willing to undercut you by this much, the perhaps you have overestimated your market.