R&D, Marketing, image, sponsorship but mostly they will charge what the market will bear based on the perception of the product, it's manufacture and the company history.
I understand your use of the auto market as a comparison but it is not truely acurate. No car is assembled by robots. The shell body is welded by robot lines but final assembly is primarily done by hand or with manual assisted equipment. The main difference is that a Bentley is assembled by one or two people over the course of several days where as a mass produced vehicle (insert manufacturer of your choice) is assembled by one hundred people at a pace of a few hundred a day. Also, the tollerance requirements for parts and components and their reject rate come into play as well when determining quality vs cost. Which I am sure is true in time pieces as well as cars.
In the end I am with you....hard to justify the cost....so I don't spend it