Actually, he didn't -- Washington did. It was the first and last time a President of the United States put on his old military uniform, climbed into a saddle, and led troops into the field in person.
The rebellion was quelled more than crushed, certain guilty parties were punished, and Hamilton, who accompanied the Militia Washington had called out, was politically rebuffed. His excise measure was quietly taken down and not reimposed in the form he had intended.
Hamilton's "don't tax you and don't tax me; let's tax that fellow there under that tree" measure was actually an industrialist's tax on agrarian crops, disguised as a tax on distilled spirits, and therefore a foreshadowing of the NewYorky-grabby, chiseling impulses that produced, eventually, the American Civil War.
Having no ready access to markets for their surplus, the trans-Appalachian farmers had taken to distilling their grain into a more-transportable, value-added form and barging it down to the river towns in the Mississippi Valley. It was a good solution for a low-infrastructure situation. Hamilton's tax was an attempt to rob out the fruits of their ingenuity, labor, and risk-taking and appropriate them for his Treasury. Heard anything like that lately?
Washington left after reveiwing the militia force in Bedford, returning to Phila. and leaving operational command to Hamilton.
Two ironies; the major uprisings were in Washington County where Washington had extensive landholdings; many of the farmers protesting the tax were vets of the Rev. War and had received land grants in return for their service.
Land in Wash. Co. is not necessarily suited to agriculture; its hilly, rocky and heavily forested. Nor is there the deep top soil of the Lebanon or Lehigh valleys to the east.
You are correct about the difficulties of getting agricultural products to market, however, in 1794 there was very little market down river, the markets were over the mountains to the east. Altogether it was a hard scrabble existence and they were taken advantage of by the eastern elites.
Note that the militia force sent out numbered about 13,000 men. That exceeded the county's total population. The suspected perps were rousted out of bed in the middle of the night and thrown into filthy holding pens and kept there. Men that were in anyway involved were force marched over the mountains (in the winter) to Phila. The actual leaders took off down river to Louisiana.
Altogether a very instructive episode of centralized government and also a chrystalizing element in the development of the political parties in America.