There is a planet money podcast on this exact subject: http://www.npr.org/blogs/money/2013/02/12/171814201/episode-435-why-buying-a-car-is-so-awful

The short answer would be though, back in the early day of auto sales, the manufacturers would often strong arm the dealerships, forcing them to buy more cars than they needed. Eventually the dealerships got together and through a combination of changes to state laws and pressuring the auto-manufacturers, we arrived at our current system.

A reminder to everyone that /r/AskHistorians is not the right venue to discuss current business practices. Please stay focussed on the historical aspects of the question at hand.

You might be interested in this post I made covering auto sales in the early days of the industry.