The Federalists were deemed conservatives and focused on industry building and addressing the needs of rich merchants and landowners. The party also tended to favour Great Britain in foreign affairs ("Columbia Encyclopedia").
On the other hand, the Jeffersonians, which later became known as the Democratic party, led by Jefferson were more concerned with the ideal of an agrarian society of yeoman farmers and adamant to expand the powers of the federal government. The party also sympathized with the French. (Wright)
Hamilton's proposals including the funding of revolutionary war debt, federal assumption of the obligation of the states, creation of a national bank and federal encouragement of native manufactures were intended to emulate Great Britain's economic model. But then, such proposals leaned towards wealthy men and substantially indebted regions over others. Jefferson along with James Madison viewed these as contrary to republican morality, which promoted harmony among the different regions and closing the income gap between the rich and poor ("Encyclopedia of American History").
As each political leader attracted supporters, the national-level disagreements trickled down onto local issues.