Jefferson cut the budget, eliminated the tax on whiskey, and reduced the national debt by a third. He got re-elected.
The policies I assume you are referring to had to do with America staying out of the Napoleonic wars. Yes, the embargo decision was unpopular, but we stayed out of a war.
No we didn't stay out of the war. We eventually went into the war, totally unprepared and lost most of the fights, because Jefferson and Madison wanted to depend on militia to fight against veteran combat troops and privateers to take on the Royal Navy.
The British were stopping our ships on the High Seas, taking our people off, and forcing them into the British Navy. Some of them were British deserters, but many were American citizens. This was an act of war, but Mr. Jefferson had ensured that we were incapable of doing anything about it, by reducing the Navy to a mere pittance and virtually eliminating the professional army. The number one job of the president is to ensure the security of the nation. President Jefferson and Madison could have at least started a small but professional army of 20,000 or so, enough to at least threaten Canada if the Brits didn't cease their warlike actions at sea.
Jefferson was no fool, so he had to know that the possibility of war with Britain or France existed. Yet very few coastal fortifications were made, no improvements to the army were made, and the Navy was laid up in ordinary. This resulted in our Capital being burned, and the only reason that British were finally stopped in that campaign was due to Fort Mchenry which was built during the Adams administration. In truth, we were lucky that the Brits didn't decide to seriously pursue the war after Napoleon was defeated. But had the Brits seen us as a potential threat instead of a militia based army, we might not have even needed to go to war.
Also, there was the actions against the Barbary pirates. The Navy that Adams had started was barely enough to function in the Barbary war, but in the end Jefferson paid the bribe, and laid up half the ships that we did have. It was only after the Naval building program started during the War of 1812 that we had enough of a fleet to finally and properly deal with the Barbary pirate threat in 1815.