Some historical perspective:
Long before PSU Joined the Big Ten:
1) I used to live in "Chicagoland" in the 70's and I remember Ohio State and other Big Ten fans complaining that Michigan was sort of "teacher's pet" within the conference. There was particularly a common complaint about offensive holding and one time OSU coach Woody Hayes, IIRC, had his D-Line wear tear-way jerseys during a OSU-UM game to prove a point.
2) Meanwhile, as an independent PSU had two or three undefeated seasons without being named national champion. Thus led to long-time PSU fans having something of a persecution complex.
PSU's entry into the B1G did not go smoothly
1) This was decided by the presidents without informing the ADs, some of whom were against having PSU join. the result was that Penn State was not exactly welcomed with open arms by the rest of the league.
2) Anyone who was a PSU fan from 1993 on can list off several instances of weird/bad calls going against PSU, especially against Michigan and, to a lesser extent, OSU. Combine the 'red carpet treatment' we received when joining with the persecution complex we carried with us to begin with and it's not surprising PSU fans often suspect bias. Stories of one ref in particular who was an open UM fan being allowed to ref PSU vs UM games were going around.
3) The Sandusky Scandal obviously didn't help us. There is likely to be a subconscious bias against PSU from some officials that carries over because of that. "You're lucky to even be playing", one ref once told a PSU player who questioned a call.
So for those of you from other fan bases who log in here and wonder why all this crying, this is some of the back-story.