Experienced academic readers usually read a text with questions in mind and try to relate it to other possible approaches, while inexperienced readers tend to adopt the question of a text and the frames of the argument and take it as a given. What good readers can do is spot the limitations of a particular approach and see what is not mentioned in the text.
As you get better at reading and taking notes, you train your mind to ask questions of the text and see if it has the answers rather than seeing the text as already having all the answers.