Teaching him the structure of the subject

At this point I asked the student if he really did know the conventional answer to this question. He admitted that he did, said that he was fed up with high school and college instructors trying to teach him how to think, using the "scientific method," and to explore the deep inner logic of the subject in a pedantic way, as is often done in the new mathematics, rather than teaching him the structure of the subject. With this in mind, he decided to revive scholasticism as an academic lark to challenge the Sputnik-panicked classrooms of America.

Hi,

Could you throw some light on the bolded part in the above? I guess I know the litteral meaning. What does "teaching the structure of the subject" refer to? Thanks.