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.
At the time of the Whiskey Rebellion, there were only 3 banks in the entire country, and they were in New York and Philadelphia. Money did not circulate on the frontier.
The US had not yet begun minting our first coins of gold, silver and base metals. Some states had minted coins, but most money circulating in the cities was gold and silver of British, French or Spanish manufacture. The newer coins had known values. Older coins had been clipped so many times that a merchant would weigh the coins to assign a value before accepting them.
On the frontier it was worse, and there was an established barter system in place based on alcohol. The smallholders of Kentucky or western Pennsylvania preserved the value of their orchards and fields by fermenting the products thereof. A barrel of beer, ale, stout or porter -- or a cask of brandy or whiskey -- had a known value when bartered for a side of bacon or a barrel of flour.
The tax on whiskey rankled because it struck right at the financial core of frontier life: There was no money in the sense we know it. It reminded people too much of the British "revenooers" who knocked down doors to collect taxes for King George, and people had just fought a war for economic self-determination so as to put an end to all that. Hamilton and Washington picked western Pennsylvania for a test case because, had they picked Kentucky, the secession question would have opened up a whole lot sooner. The fix was in as far as western Pennsylvania was concerned.
The tax on whiskey showed questionable judgment.