Listening to the news reports and other blogs, you'll hear reporters and writers pontificate that Penn State fired Paterno because of the moral obligation it has as an institution. They'll talk about how Paterno failed to protect the victims and didn't completely fulfill his duties as the head football coach and as one of the most powerful people at the university. Another writer on this site, Gotti, wrote a good article detailing the callousness of the "protesters" of the firing.
However, the real reason why Paterno got fired is the same reason behind the NBA lockout as well as almost all business arguments: money. Most people have this utopian idea that universities are higher-learning institutions that conduct independent research and educate our young adults before they are sent out into the real world. I regret to inform you, that isn't the case. University presidents and provosts are primarily measured on their ability to raise money. The more money the university has, the better you can pay professors/coaches, provide state of the art research/athletic facilities, etc. Universities get money in various fashions, but one big way is through donations.
The thing about the Paterno case is that the worst part has yet to happen. We have seen some horrific details from the grand jury testimony and the stories about what the graduate assistant witnessed. However, we have yet to hear everything the prosecution has up its sleeves. To get the indictment, the prosecution only had to show enough evidence that there is reasonable suspicion that the crime the accused is being charged with had occurred. It is a pretty low standard of burden for the prosecution. Given that, there is no reason for the prosecution to show most of its hand. Certainly during the trial, more details will come out and as that happens, people will start looking at the people in charge at Penn State and how they could have possibly missed these horrific acts. While this negative attention will be bad enough on the university, it would be exponentially worse if people such as the president, AD and yes, the head football coach are still at the university. Like it or not, these positions come with a certain level of responsibility and the individuals holding the position are held to higher standards.
In order to limit the hit on donation amounts and research grants being conducted at Penn State, the board of trustees had no choice but to clean house and distance itself as much as possible for this atrocious incident. We can applaud the board for "doing the right thing" but make no mistake about it, if it was financially beneficial to keep Joe Paterno and/or the president, they board would have done it. As always in business (yes, universities are businesses), follow the money!