Traffic engineering is one of those fields where there probably haven't been a lot of hobbyists, until recently, when the Internet has allowed geeks to become expert on pretty much any subject with a few weekends of study. I would also imagine that the PE licensing rate among practicing traffic engineers is pretty close to 100%, whereas I have yet to meet a PE-licensed software engineer... I'm sure the half-dozen or so licensed engineers at NCDOT were probably pretty freaked out to see a study like this from an amateur. Who knows, maybe the group did blow a lot of the conclusions -- it's almost certain that Cox's team disagree with the report, since it is counter to their recommendations. Anyway, the last thing the state engineers want to do is to validate the standing of the community group by engaging with them on the issues, even if it's to educate them on where they made mistakes, so they're going to look to discredit them.
As an analogy, practicing medicine without a license is a crime, even if you're really good at it, and even if all of your patients know you're not licensed.
Again, I think this is a terrible way to try to solve the problem, even if it is supported by laws or regulations. Professional fields of all kinds need to cope with the fact that organized groups of laypeople are going to be able to mount credible challenges to their opinions, on their turf and using their tools.