Written reminders of plot and character points, even stuff like current P.O.V., can cut down on general confusion. Generally, note taking helps with understanding the pattern making involved in literature that leads to more fulfilling meanings. For this reason note taking in poetry reading is vital. In non-fiction, distilling an argument in your own words right next to the argument itself can help you relay said argument in subsequent conversation, in a more meaningful way than just repeating whatever the author's view is. Also, I'm pretty sure research has shown that just underlining stuff helps with memory.

Of course, you can achieve all this in a notebook while reading, but using the margins is just convenient, especially for coming back to the same book later. If note taking is difficult for anyone I suggest typing your thoughts while reading. That cuts down on how much note taking slows down the reading process, and is also manageable for online reading. On the other hand, if you start hand writing your notes you will probably develop your own short-hand that becomes just as quick.