But Governments are neither homogenous nor monolithic. Saying 'Governments do X' is like saying 'corporations are at the root of all our problems.' Reason along those lines, and pretty soon the only rational choice is to become a hermit and avoid society entirely. After all, society is made up of people, and people are well-known to engage in murder, rape, robbery, etc. etc. Therefore, people are the problem.
If someone is engaging in murder, rape or robbery, it would make sense to call attention to this fact, and then perhaps do something about it, wouldn't it? Parts of the US government are CURRENTLY misusing the word "terrorist" as a very broad label. This is very dangerous for the reasons discussed above. It's important to call attention to this problem if we have any hope of halting it.
Yes - you call attention to the specific person engaging in those acts. When you overlook that requirement of specificity, you end up accusing people based on their membership in a class, eg 'all gypsies are thieves, X is a gypsy, therefore X is a thief.'
So saying 'the US government is doing X, and I think it's acting illegally because Y' - fine. But 'the US government is doing X and this will end badly because governments always oppress citizens' (an argument that has appeared here a lot lately) isn't fine, because it rests on a false premise.
It's clearly useful to describe a structure independently from its consitutent atoms. Anyone who doesn't do so is virtually unable to communicate.
Social structures do things, and are amenable to institutional analysis. This allows us to act without omniscience. Institutional analysis allows one to analyze institutions independently of individuals; replace all the people, and you may nevertheless expect similar outcomes. Thus we can perform institutional analysis on governments, corporations, mafias, economies, consumers, managers, startups, etc.
If this weren't the case, humans wouldn't form institutions in the first place.
I wholly agree, but surely you've noticed that many people take the observation that 'some governments sometimes do things' to mean that 'all governments inevitably do those things,' which is plainly untrue.