Scout and Jem consider Boo scary at the beginning of the story because he never leaves his house, they later learn that it is Boo who is afraid. They have ascribed him mythical monster status, and make up stories about him based on what little they know. The mystery is part of the fun, of course, but they are also drawn to Boo’s story of pain and suffering. On a subconscious level, they realize that Boo is a victim. He also symbolically represents their childhood. As a child, everything is mysterious. When you grow, you realize that the monsters are not the people who hide in their houses. People hide in their houses because the monsters are outside.
It takes a monumental event to bring Boo out of his house. When he sees Jem and Scout, he is drawn to their innocence. He wants to be a part of their world, and he does this by leaving the presents for them to find in the tree. Boo has a childlike innocence, and these overtures are peace offerings. He also begins actively involving himself in their lives when he mends and returns Jem’s pants. This foreshadows the time he will literally save them at the end of the book when Bob Ewell attacks Scout with a knife. The world actually is a scary place, but Boo is willing to risk it for Scout. This is the reason Atticus and the sheriff decide to protect him, so he will not have to become a part of the real world.
Boo's story is another example of how people's intolerance affects others. Because Boo is different, he is ridiculed. He is actually different because he suffered long-term abuse at the hands of his parents. Boo is a victim, both of them and of society.