One night in Naomi there's a huge, terrifying thunderstorm. It soon becomes clear to Opal and her father, the preacher, that poor old Winn-Dixie is scared out of its wits by this natural phenomenon.
The preacher explains to Opal that Winn-Dixie has what's called a pathological fear of thunderstorms. A pathological fear is one that goes beyond normal fears, something that you can't be reasoned out of. Some people have a pathological fear of spiders, hypodermic needles, or flying. But in the case of Winn-Dixie, the poor dog's petrified of thunderstorms.
Opal's worried that her father won't want a dog around that has such a fear and goes crazy during thunderstorms. But she's surprised when he allows Winn-Dixie to run back and forth between his room and Opal's until the storm subsides. As Winn-Dixie's fear of thunderstorms is pathological it cannot easily be fixed—or maybe fixed at all. But it is nonetheless possible to make the poor dog feel a little less petrified whenever a storm breaks overhead. And that's what Opal's dad is doing by allowing the dog to run around the house.
As Opal and her dad curl up on the couch with Winn-Dixie between them, he tells her that they'll have to be extra careful the next time there's a thunderstorm and keep Winn-Dixie inside the house so that he'll be safe. This is the only realistic way they can handle the dog's pathological fear.