1) The requirement of a food handling license for every employee is not a trivial problem. It completely distorts the market for hiring, really making it almost impossible to do legally. Remember, this is not the kind of job where people stick around for years so a 2 month lead process in hiring is tolerable. And it's not like this food handling license is in any way helpful to maintaining the public health; its not required for regular restaurants (for every worker like in food trucks).
2) In reality there are next to no legal spots to park a food truck in nyc. In manhattan, pretty much every spot is metered, and therefore illegal. However, as long as no one complains, usually the cops leave you alone. Usually, but its unpredictable.
3) Arbitrary and capricious enforcement of health regulations by health inspectors that can lead to large fines and confiscation of your permit. Again, don't underestimate how big a deal this is. At any time, for approximately any reason if the inspector doesn't like you, your entire business can be shut down. Think about how patent lawsuits affect startups and then imagine that a class of patent inspectors can just bust in unannounced several times a month to shut you down. It's like that.
4) You can't actually get a permit legally because the city doesn't issue them any more. All food trucks get their permits on the black market and the costs is up to $20K per year now. It's not just the cost but also the hassle of having to deal with that. It's also completely stupid from the city's perspective as they could be auction off permits as they do for taxi medallions. Instead the benefit goes to people who just happen to have been issued a permit many years ago for $200.
5) You must park in a licensed commissary as mentioned in the article. It means you basically have to pay 3x in rent what you would if you could park legally in a private lot. And plus those places are actually completely filthy. I've been to several.
All that said, the article is actually quite wrong about it not being a profitable business. The people I know are raking in cash hand over fist. There is huge demand as long as your food and concept are decent. If the city actually fixed some of these regulatory issues, there would be a huge explosions of trucks overnight.