I don't see that as hypocrisy. Pounding small schools into the ground for small violations while delaying and delaying and delaying and delaying major investigations into major schools is hypocrisy.
IF the NCAA were working optimally for it's intended purpose, that purpose isn't to "protect" student athletes away from the field/arena/course/track/etc. The NCAA can "protect" student athletes by adjusting and enforcing rules of competition. Things like horse collar tackle and targeting penalties were added to football to try to take away forms of play that can cause injury. Requirements for facilities, such as basketball courts, can help prevent injuries. Nothing the NCAA does will eliminate injuries during athletic competition because athletic competition is inherently dangerous. Even in something seemingly benign like sprints can have muscle pulls or falls that need extended medical treatment. The NCAA, even if working perfectly to try to prevent injuries will not prevent injuries.
Away from the field, what is the role of the NCAA in "protecting" student athletes? Should the NCAA prevent SAs from being involved in a car accident? How could they even do such a thing? Should the NCAA prevent of-age SAs from drinking a beer? Should the NCAA prevent SAs from having unprotected sex and getting an STD? If the NCAA even attempted to do the last couple of things there would be all kinds of civil rights violation accusations, at least against the public schools.
When I was in high school I played D&D. (Yes I was a geek, and I still am.) Our high school principal read some Christian material that said the D&D was not really a game, but actually a cover for "Devil worship". (I am a Christian also and not knocking the religion.) He announced that anyone who played D&D would be expelled from the school. He was mistaken about the game. Even if he had been correct, and we all were Satanist, it was a public school so he couldn't have kicked us out. He tried to insert himself into a situation over which he had no authority, and it only ended up making him look like an idiot. There may have been some parents who thought he was doing the correct thing, "protecting" the students, but he wasn't actually.
My general idea is that the NCAA should stay in it's lane and concentrate on athletics, athletic departments, recruiting, and educational requirements to be involved in NCAA sports. It is fine for the NCAA to have educational materials and marketing programs to educate SAs about: Dangers of DUI, risks of risky sex, how to handle money, etc. However, the NCAA has no authority regarding any of those items and they should not try to insert themselves into an authoritative role in such matters.