The main reason I do it this way is because when you use a linear format rather than pieces radiating out from the center, the brain imposes a hierarchical structure on the content, regardless of whether one was intended. And this matters. It changes, even if subtly, the way you process and understand the material. Another thing mindmaps let you do is make connections between different nodes; something that's especially hard (or impossible) to do with linear notes.
That meant, however, that there was a serious mismatch between what they were being asked to do-- fill out mind maps-- vs. what they could do--type linear notes into a text editor or outliner.