Not saying that's a good reason, just pointing out there's a lot of money and interest in keeping the status quo, as there always is.
From what I have heard, many of these franchise laws date back to the Great Depression, when manufacturers were forcing dealers to buy cars that the dealers could not then sell.
(There was a recent NPR Planet Money episode on exactly this issue, but I can't find a complete link. http://www.wbur.org/npr/172402376/why-buying-a-car-never-cha...)
http://www.npr.org/blogs/money/2013/02/12/171814201/episode-...
The NPR page also references this paper which goes into a lot more detail, but if you can't listen to the podcast it's a good reference.
http://faculty.som.yale.edu/FionaScottMorton/documents/State...
TLDR: Automakers and their dealerships have lobbied to get laws into place over the last century to ensure that those laws favor car dealers and their preferred way of operating. It will be extremely hard to change the status quo.
I think the reason has to be purely political: it stands to reason that state politicians would benefit more by protecting a local franchise vs. a national car company (even though it is ultimately detrimental to their constituency).