Google can point out some allegedly biased reporting they have done [1], but I'm certainly no expert on it. My concern, in this particular case, is that Mother Jones has, by most accounts, a left-leaning bias [2, among others]. Dealership associations have, by most accounts, a right-leaning bias [3, among others]. The conflict there raises my internal alarm when reading them on this issue.
Moreover, you can't talk about franchise protections without talking about two major recent presidents during their tenure as governors. That those presidents are generally referred to negatively by MJ (in my personal estimation) and that casting their political legacies in a negative light makes a naturally-appealing target, needs to be considered.
That said, I agree with you. I find MJ's articles generally good and I believe their reporting on this issue was very enlightening.
[1] https://www.google.com/search?q=mother+jones+bias
[2] http://www.allsides.com/news-source/mother-jones
[3] http://fivethirtyeight.com/features/news-flash-car-dealers-a...
Essentially, California pioneered the idea of protecting existing franchises from being cannibalized by the manufacturer that they were dependent on. But other states have taken the idea to an extreme.
[1] http://motherjones.com/politics/2009/02/why-you-cant-buy-new...