Consider the case of a blog. Each blog post has many comments. Each post has an author, and each comment has an author. Some of those entities may have dedicated URLs, and others may not. Additionally, the authors are highly repetitive; you want to refer to them by identifier, not by embedding them.
Because a tree of data can be represented easily as a graph, but not vice versa, JSON API provides a straight-forward way to provide a list of records that are linked to each other. The goal is simple, straight-forward processing regardless of the shape of the graph.