Tolls achive more than just crudely approximating a car's impact to the road system. Tolls can influence traffic behavior and congestion; which I'd guess is the point of that LA article.
Also, I'm curious how those costs look when you have open road tolling, as recently implemented in Massachusetts. No toll takers, just cameras, computers, and a call center "somewhere".
[1] https://news.ycombinator.com/item?id=13817279