Brick and Mortar establishments have costs associated with starting up. Food Trucks have start up costs. Part of that cost is obtaining the proper government approvals. Simple reality to start a business. Not saying Gov fees are good or bad, just the current reality.
The premise of the OP is that the government fee on Food Trucks is the only barrier to entry. Any cost associated with starting a business can be considered a barrier to entry. If the fee on Food Trucks is dis-proportionate compared to brick-and-mortar, that is not right. However, if $1000 is too much for some Food Trucks, maybe they are not properly capitalized in the first place. Think the restaurant business, fixed or mobile, is easy? Guess again.
Didn't read the article did you? It's more than a $1,000 fee.
Trucks that pony up in Noblesville still face restrictions, including bans on parking in the downtown zoning district, in residential areas or within 1,000 feet of special events and the Noblesville Farmer’s Market.
Downtown advocate Renee Oldham, executive director of the Noblesville Main Street organization, endorsed the zoning ordinance, calling it a compromise that offers existing eateries some security while giving residents more dining diversity.
Food trucks work when there's a population density nearby of which they can take advantage. The zoning restrictions would keep them away from areas with lots of pedestrian traffic. One of the operator who pays the fee in Fishers noted that. Also from the article:
Nickander said it takes time for a food truck to build a following, making the high cost a barrier to entry—especially in a suburb that lacks the population density of a city like Indianapolis.