Those are reasonable thoughts. It's the not knowing of how much Paterno knew or didn't about JS over the years that's got everyone turning on each other. A grown man doesn't just all of a sudden wake up one day and begin molesting underage people. JS had been in and around that program for nearly 40 years even if he wasn't committing crimes every day, week or year, he'd been doing it at least off and on for a long time and when you've been at the same place for that long of a time, people know things--and they talk. That's how journalists have a job and those things get back to people. It's just hard to believe Paterno didn't know, or at least hear rumors about JS over the years. I'd bet the assistant coaches over the years knew/know things and are not talking to protect the program still.
But Paterno did do what he was supposed to do but like you said, he had influence, maybe not over the entire school, but that program was his and the take the public has on him, for which he is responsible for building up, is that he knew what was going on about everything.
Like the other guy said up above, Paterno selfishly stayed on too long thereby, putting himself above the program as the years went on and put the program above all else. It doesn't make any sense for school officials to give JS the keys to the house after all those years. There's just too many unanswered questions and that's why articles like that are written. Especially after JS retired when he did, when many felt it was before his time to do so.