Northern manufacturers wanted high tariffs on manufactured goods and low tariffs on agricultural products. Southern farmers wanted high tariffs on agricultural products and low tariffs on manufactured goods--to placate Europeans so they'd buy Southern agricultural products, and to check the economic power of the North. And of course the Federal government relied on tariffs for income--the Articles of Confederation being considered a failure largely because the Federal government had no independent source of income--and as a foreign policy tool.
Everybody was at odds.
(Note that it was also common back then to impose export tariffs, which added considerable complexity to the debate. Today export tariffs are largely unheard of in the U.S. but perhaps ripe for rediscovery. Though we recently loosened restraints on the export of crude oil and natural gas, so it probably won't happen any time soon.)