When you select Auto Navigate, the Database Navigator lets you view the associativity of objects that you select from the tree list and any objects listed in the window on the right. For example, if you have a model with a joint motion, and then select to view the associativity of that motion, you see a joint listed in the right window, as shown below.

With Auto Navigate selected, you can just select that joint from the right window to view its associativity. If it were not selected, you would have to select the joint from the tree list to view its associativity. In addition, when you select the joint in the right window, the Database Navigator also highlights it in the tree list.