The government itself is the agreement of the states to work together, the documents pointing out all the rights and responsibilities and limitations, the system by which the states elect representatives and a president, and the judicial system.
The current instanciation of the government is what many people attack when they're talking about government, and what many people mistake for the government itself. That's the people currently in office, and the laws resulting from the current interpretation of the founding documents.
So, if someone says it's an inherently flawed system, that the Constitution is bunk, that there's no earthly way you're going to get a good government out of that setup ever, I could understand some outrage from Diehard Patriots. However, there are people who criticise the system who don't get half the flak that someone saying, "The current president is an incompetent moron with halfassed policies, and a sockpuppet or a chimp should be able to do a better job," does. (Well... or something like that.)
The thing is, the documents have a lot of room for freedom in them, and are vastly open to interpretation by the leaders, especially against current societal trends, whatever they are. People mistake the traditional laws that have build up as the result of current societal needs for the framework itself, and interpret any attempt to remove the non-current, irrelevant, and actually sometimes harmful as an attack against the foundations of the government, when it's actually more like pulling off some siding that's rotting and very out of style.