What do the owls in the book Hoot symbolize?

The owls in Hoot are symbolic on at least three levels. Most obviously, the owls symbolize wildlife and natural habitats that are at risk of extinction or harm from residential and commercial development. Of course, this is literally true of the burrowing owls on Mother Paula's property, but it represents the larger issue of beautiful and unique creatures that are threatened by loss of habitat. After Roy's family goes on a Sunday outing to the Everglades, Roy gets an idea of what the crusade to save the owls represents. He reflects, "It wasn't just about the owls, it was about everything—all the birds and animals, all the wild places that were in danger of being wiped out." 

The owls also represent Mullet Fingers, or Napoleon Bridger, himself. Like the owls, Mullet Fingers is associated with nature. He feels at home in nature and has a love for and an ability to connect with wild creatures. He is small, but he is unique and special, just like the owls. Yet, like the owls, he is considered a nuisance by those in authority. His mother sends him away because she doesn't want him; Curly continually curses the owls because of their burrows, and Chuck Muckle is ready to ignore the owls' fate. Mullet Fingers identifies with the owls so fully that he digs himself into an owl burrow on the day of the grand opening, and Hiaasen completes the connection between Mullet Fingers and the owls by having an owl land and perch on his head. 

Finally, the owls represent the children in Roy's community whose natural habitats are threatened, that is, who don't belong to loving families as each child deserves. Mullet Fingers and Beatrice's parents are both dysfunctional and either neglectful or abusive. Although she is a school guidance counselor, Garrett's mother seems to put all her effort into her job and none into properly raising her son. Dana Matherson's family is as violent as he is; his mother gives Dana a fat lip. Only Roy seems to enjoy the nurturing environment of a loving family.

The symbolism of the the owls in the story advocates not just for the protection of animals, but also for providing a proper environment for young people as they are growing up.