Here is the reality of the situation. I don't care about the neverending Sandusky debate namecalling nonsense, so leaving that aside...
As far as fanbases being nice to each other and which side has bigger a-holes:
The problem from the Rutgers fan perspective is that many of those who are part of large visiting fan bases, especially Penn State, adopt this infantile mindset that part of the fun of attending the game is intimidating the home team's fans by being there in large numbers and yelling as loudly and obnoxiously as they can, instead of simply focusing on and cheering in a reasonable way for their team. Penn State fans in particular have their "We Are" chant, which is by its very nature (despite what Penn State fans might say) designed to be obnoxious and to provoke irritation in the other teams fans. From the idiotic way it sounds when one 40 year old dude yells out "We Are" (always sounding like those are 2 of the 11 or so words they know how to say in English) to the giddy, full-throated response, it is part an expression of support for their team, and part a childish attempt to annoy and "dominate" the scene of the game. These are mostly full-grown adults, mind you, who derive much of their self worth from feeling associated with a college football team, and by being able to adopt the stance of a "winner" and "bully." Of course all of this is rooted in the inferiority complexes these people deal with in their own lives. Rutgers nor other fan bases are immune to this, but it is particularly distilled in Penn State fans.
Then you have their coach, who for his own reasons wants to amp up this factor of "invading" the other teams stadium, and it all adds up to turn what should be a college football game into a "war" with an "invading force". It should not then be any surprise that there will be hostility involved, both provoked and unprovoked. Let's please not pretend that if Penn State were on their way to a 2-10 season and Rutgers was riding high, and 25 thousand Rutgers fans attended a game in State College, that there would not be unprovoked hostility toward Rutgers fans at the game.
Of course there will be always be people on either side that want to act like douches to other fans that are minding their own business. I can't speak for them and they have to answer for themselves.
Anything else beside the above is just spin coming from either side. My advice is for people to mind their own business and worry about themselves, otherwise you reap what you sow.
