I think you're wrong about that. Yes, the Whiskey Rebellion was directed at the government -- but certainly not the government that the U.S. Constitution "produced."
In the minds of those who took part in the rebellion, the excise tax on whiskey that was passed by Congress in 1791 was a blatant violation of Article I, Section 8 of the U.S. Constitution ("The Congress shall have power to lay and collect taxes, duties, imposts and excises, to pay the debts and provide for the common defense and general welfare of the United States; but all duties, imposts and excises shall be uniform throughout the United States . . ."). By taxing one specific type of alcohol (whiskey) while exempting others (wine and ale), Congress was acting in a manner remarkably similar to today's anti-tobacco Nazis -- they taxed the stuff that was produced in the rural western parts of the states (and served as a major source of revenue for farmers who worked the poor soil of the Appalachian foothills), while exempting the stuff produced consumed by the majority of the people (voters) in the more densely population areas along the seaboard.
The farmers in western Pennsylvania, Virginia, and North Carolina took one look at the excise tax and said, "Bullsh!t -- as far as we're concerned, you bastards in the Federal government are no different than the British bastards we threw out of this place not that long ago."
Thus opened a rift between the rural farmers of Appalachia and the dwellers of the more heavily-populated areas along the coast -- a rift that eventually generated the moonshining industry, stock car racing, and a clear divide in the 2000 presidential election between what we now know as "Red" and "Blue" areas of the country.