I'm not aware of how he was perceived by the American population in general, but I've read that before the Louisiana Purchase there were fears that he might attempt to re-establish a major military presence in North America. His troops had put down a revolt in Haiti, and it would have been simple to ship the French army over to New Orleans and from there take possession of Louisiana, which would have blocked the westward expansion of the United States. Southerners apparently feared that Napoleon would free all the slaves in Louisiana, which could trigger slave uprisings elsewhere. These kind of tensions were presumably eased after the Louisiana Purchase.

Then in 1808 came the Bayonne decree, when Napoleon ordered the confiscation of every American ship putting in at a French port. After Napoleon's abdication in 1814, the British were free to redirect their military forces to the war in America.

So it seems as though Jefferson and the American government may have been rather wary of Napoleon, but willing to play him off against the British, and one can expect this attitude to be reflected in the population at large.