It only will make sense when you reintroduce the idea of "the political" into your framework. Without that, a government is simply a territorial administrative apparatus or provincial satrapy. If your parents are Canadian, perhaps you are as well (or at least very familiar with Canada), and can relate to a government seeing its population as simply interchangeable units of administrative responsibility managed by a hedonic rationalism. I think Canada is a great example of what US voters in the last election don't want to be. It's kind of a nice, albeit cold, place but very authoritarian and prone to treating its identity as something of little value and an embarrassment, except contra the big bad United States next door. Canadians look at our health care system and school shootings and suppose their system is obviously better, but Canada comes across as very naive and ungrateful for the benefits it receives as our northern neighbor. I suspect there are many Canadians who also don't like their government's policies but are at a loss on how to effect change because their government is less susceptible to populist political waves than the US.
The government works in some areas and not in others. Our once envied university system has become a human gristmill cartel, indenturing a generation of our youth under debts they will never dig out of because of perverse incentives engineered via vast federal spending programs. Foreign students may still come for the prestige but many diplomas are effectively worthless and many schools properly should be mothballed. In any case, measuring a government's worth by how many people receive benefits is a pretty pathetic standard. It's beneath human dignity to have such meager aspirations for a country.
Unaccountable civil services aren't hard to understand in history. Like a military that is ostensibly under the control of the king or president but not really, so have civil services sometimes constituted as separate government that can just ignore the commands of elected representatives of a people. Laws can and are passed to entrench the civil service even deeper, making it hard to fire any but the top-level appointees. These can try to get the institution to do something differently but if the institution is unresponsive they can rant and rave all day, the careerists can just wait them out. It's not hard to understand if you study incentives. They are deeply misaligned and it is only because the administration learned some of these lessons the first time around that they came in with a much more effective game plan this time. You can see how dramatic actions are required to overcome the institutional resistance. I'm sorry that good people have/will lose jobs, but government should not be a tenured jobs program. The taxpayer doesn't have that luxury, why should this subgroup? Why should we all engage in a fantasy that federal employees aren't people who, sometimes despite the best of intentions, are going to pursue their group interests even at the expense of other groups? Huge pots of money are going to attract huge pressures from outsiders trying to access funding. Many of the high profile grants to ridiculous projects are not surprising when you see these institutions as participants in political patronage networks. There has to be some way to officially distribute the money. Have them dig and fill holes or put on puppet theater for the blind. It doesn't really matter.
Keep in mind there is no ultimate fix for this. All institutions decay and need to be replaced from time to time. Getting upset about this particular patronage network being disrupted is the wrong worry unless you were a particular recipient of its largesse. If not, then you might come out better off at the end of the day.