Even without what happened at PSU, Paterno is not well liked as a QB coach.
They have somehow managed to land several highly ranked QBs the last few years, none of whom have panned out as of yet. They have had some decent QBs since 1994, but only 5. That's a big whiff over 16 years. Michael Robinson, Rashard Casey, Zach Mills, Kevin Thompson and Darryl Clark were all excellent. That's 8 out of 16 years of competency. Not good enough. But Anthony Morelli, Paul Jones, Kevin Newsome and Ricky Bolden were top 5 QBs in the nation. Jones is yet to get a shot but I don't hold out hope.
More important are all the QBs that Penn State has lost. Chad Henne was a longtime PSU fan and PSU lean, the staff was shocked when they lost him. Chris Simms too. It was because of Jay that Henne ended up at Michigan.