Because it's a waste. Pfizer has the comparative advantage in marketing drugs, and NWU in researching them. Econ 101: both parties are better off trading.
If Northwestern did the research with its own money (which does sometimes happen, I think), then it is good that Pfizer had to pay Northwestern for the research, because this funds more research. The patent is just the legal mechanism that makes Pfizer have to pay as opposed to getting the research for free.
In some cases, the government funding issue is relevant. Not in all cases.