On the whole of things, Scout is brave young lady. She stands up for what she believes in and is willing to fight for it. She is not immune to fears though.
Early on in the novel, the reader learns about Boo Radley. Because the story is told from Scout's perspective, the reader is given information about Boo that she believes to be true. To Scout, Boo is essentially the creepy neighbor that every kid has grown up with. She thinks of him as a "malevolent phantom." A guy that creeps around at night and peeks into the windows of sleeping children. He's a scary guy at the beginning of the novel, because the reader knows so few real details about him.
Relating to Boo is another fear that Scout has at one point in the novel. In chapter 6, Jem needs to attempt to sneak back into the Radley yard at night. He needs to sneak back in, because he lost his pants over there a few hours earlier. Scout genuinely fears for her brother's safety. She thinks that Mr. Radley or Boo will shoot and kill Jem for trespassing.
A third fear that Scout has is her fear for Atticus's safety. After being embarrassed in court by Atticus, Bob Ewell spits in Atticus's face and makes several threatening remarks. Scout is afraid that Bob Ewell will actually follow through on those threats.
One last fear. Scout fears any time spent at Finches Landing for Christmas.
Had I ever harbored the mystical notions about mountains that seem to obsess lawyers and judges, Aunt Alexandra would have been analogous to Mount Everest: throughout my early life, she was cold and there