The major issue in this election was the unpopularity of a number of things that the Federalists had done while in office. One of these was the Alien and Sedition Acts. These acts had become very unpopular because of the way in which the suppressed people's freedom of speech. Another issue was all of the money that had been spent and the taxes that had been imposed to prepare for a war (against the French) that never came.
Knowing they were losing, the Federalists went after Jefferson on cultural grounds. They accused him of being an atheist and a supporter of the worst excesses of the French Revolution. They claimed that a win for Jefferson would lead to things like Bibles being burned and women raped. If Jefferson won, one newspaper says here:
Murder, robbery, rape, adultery, and incest will be openly taught and practiced, the air will be rent with the cries of the distressed, the soil will be soaked with blood, and the nation black with crimes.