It's a bit more complicated than you would think, simply due to the nature of public sector finance. In private sector finance, it's a simple bean counter's maneuver to budget some of the savings from cheaper fares to cover penalties on cancellations or changes (in some organizations, these may even fall under the same line item). If the former is significantly greater than the latter when your actuals come in, you might even win a bonus for saving your company money.

In the public sector, you can't ticket a flight or commence travel (which is an obligation of taxpayer dollars) until your travel authorization is completely approved by a transparent process established by your agency to determine that 1) the travel is authorized by Congress under federal law, and 2) the necessary funds have been appropriated by Congress for said purpose. But since nonrefundable fares often have an immediate or limited ticketing window, if you travel frequently or on rapidly changing schedules (as many of us do, in both private and public sector), it's simply not practical for the authorization process to play through before your ticketing must take place on the limited nonrefundable timeline.

Before you blame the bureaucracy, first consider that all this "red tape" is actually put in to place to protect against waste, fraud and abuse. And it works quite well, recent GSA shenanigans aside.