What is the thread in Hoot?

I think by "thread" you mean "theme," which will be the novel's central idea and message.  Hoot has a couple of central themes in my opinion.

One theme is the theme of environmentalism.  That single theme is the main "thread" that holds Roy, Beatrice, and Mullet-Fingers together.  They are trying to protect the owls that live nearby.  Those owls are in danger of having their habitat destroyed by a construction job.

That construction job...

I think by "thread" you mean "theme," which will be the novel's central idea and message.  Hoot has a couple of central themes in my opinion.

One theme is the theme of environmentalism.  That single theme is the main "thread" that holds Roy, Beatrice, and Mullet-Fingers together.  They are trying to protect the owls that live nearby.  Those owls are in danger of having their habitat destroyed by a construction job.

That construction job focuses on another theme: corporate greed.  The company is portrayed as one of the bad guys, because it doesn't care about who it has to lie to and destroy to get the job done in the name of profits.  

A third theme is the theme of friendship.  That is a fairly obvious theme because the novel's three main characters are all very tight friends by halfway through the novel.