A few things. I remember reading that article a few years ago plus a few times Sports Illustrated has written about it too. I'm not an expert but this is my understanding of how this stuff works.
1) The head coach rarely has anything to do with this stuff and is shielded from it. It's plausible deniability. Just like in politics people shield presidents and senators from things.
2) A booster doesn't need any connection to the football program to pay a kid. All he needs to know is if a kid is in town on a visit (and he can easily find this out online now) and he can magically " bump" into him. If a coach on staff is needed for help it's a GA or a position coach at the highest.
3) Players aren't given thousands of dollars unless they're already on campus. They're given a few hundred on visits to build relationships. Once a kid is on campus and playing well, then maybe they start getting more. $300 is easy to cover up or explain away. $10,000 is not. $100,000 definitely is not.
4) Some kids don't want impermissible benefits and don't take them. Some do.
If you think Nebraska, along with every other Big 10 school, isn't cheating then you're kidding yourself. The only thing is the head coach probably is not in on it. If purity in collegiate athletics is important to you, then watch D-III or NAIA.