Atticus trusts Jem and Scout so much because it is in his nature to trust people until he has a reason not to do so. He judges people not by whether they are children or adults, rich or poor, black or white, but by their characters and actions. Atticus also recognizes that the best way to build trust is to extend trust. When people feel trusted and valued, they tend to become more trustworthy and repay the respect.
While Atticus understands that his children are not always completely upfront with him about their Boo Radley adventures, he also knows that if he asks them pointedly to tell the entire truth about any topic, they will do so. He is a wise enough parent, however, to understand that children will be children and to allow them to have their space.
Rather than hovering over and distrusting his children, Atticus has built a relationship with each of them. They know they are respected and trusted, and they respond in kind.