When a student does not understand some reading material (or a lecture), it is likely that she will say that the material is confusing. Of course she would also admit that she is confused, but most likely her point is that it is because the material is confusing that she is confused.
Now if the material is in fact confusing, then there is nothing wrong with her saying so, and it is understandable why she is confused. It is possible, however, for the material to be very clear while the student is still confused. She is confused because, say, she is not reading the material carefully enough or because the material is too advanced for her.
From a third person perspective, we can make this distinction: the material is clear, but she is confused. But from the student's first person perspective, such a distinction seems unavailable. It seems incoherent for her to say, "The material is very clear, but I am confused."
Although the student who is confused cannot judge that the material is clear (when it is in fact clear), she can still entertain the possibility that the material is actually clear. If she takes this possibility seriously, then she may find it more appropriate to say "I am confused" without saying "The material is confusing".