Probably because the NCAA is on shakey legal ground with all this. There's already a report that PSU has retained legal counsel, so it might be challenged.
The reason for the stiff fine is that the NCAA's "Death Penalty" is reserved for programs that are already on probation. PSU is NOW on probation, but wasn't before the Sandusky-affair. So the NCAA is fining PSU the equivalent of 1 year's revenue of the PSU football program (interesting that they know the amount).
Giving SMU the death penalty didn’t put too many companies out of business here in Dallas. Getting rid of PSU Football would put a lot of companies out of business, and I am not certain that these penalties won’t have the same effect. But that probably was a consideration when deciding on the Death Penalty.
The cover up involved multiple levels of leadership. The criminality was so egregious that the NCAA needs to set a precedent and make an example of Penn State.