I would argue that was anti-government sentiment but not necessarily "anti-American." There are many people in the US who loudly proclaim themselves to be the "real" Americans in the same breath that they denounce any movements by the government they don't agree with.

The fact that Cap, symbol of America, was on the anti-Registration side makes it hard for me to see Millar as taking a jab at America (the myth). American government, sure, or perhaps all governmental invasions of privacy. But I don't recall anything in Millar's work that suggests to me that he was taking a sideways jab at the myth of America as a dominant, superior, always-right force. But, admittedly, it's been quite a few years since I've willingly read anything by Millar.