Hoot is a book about environmental heroism.
The Pancake House chain is developing illegally because they never got the required permit to build since the owls had nesting sites on the property.
Chuck Muckle attempts to "destroy evidence" as he bullies the construction foreman Curley to go ahead with the project. If the construction commenced, the owl nests would be buried and therefore destroyed.
Once the kids, with the help of Roy's father, uncover the lack of construction permits and the photographic evidence of the owls' nests, they were able to bring the construction of the restaurant to a halt.
The burrowing owl is on a list of threatened species and is protected from habitat destruction, poaching, or harassment. While some people may not think a bird should be protected, all species on the planet inhabit a particular niche and perform specific functions in their habitat. If the habitat becomes uninhabitable for a variety of wildlife, how long before the planet is uninhabitable for the human animal?