Keeping in mind that different people learn in different ways, there's another possible way of looking at this.
Some people learn better aurally than visually. Some remember things better by writing them down. I know a few synaesthetes who likely might learn better by using various highlighting colors. Perhaps those who highlight everything are actually helping their own brains to learn by doing this?
This said, I myself still don't understand people who are highlighting everything in their books this way. I suspect that some are just trying and imitating what they've seen before and just haven't learned to read and annotate actively.
Helping students to discover how they best learn can be a great hurdle to cross, particularly at a young age. Of course, this being said, we also need to help them exercise the other modalities and pathways to help make them more well-rounded and understanding as well.