To give some idea for our not-American friends, here's a very general, far too simplified gist of how the tax system is laid out:
* Federal taxes, overseen by the IRS.
* State taxes, separate and independent from Federal taxes and overseen by the governments of each State.
* County taxes, mostly separate and independent from State taxes and overseen by each county's government.
* Municipal taxes, mostly separate and independent from County taxes and overseen by each municipality.
Taxpayers need to file their taxes with the IRS (Federal), their State, their County, and if applicable their Municipality. No, these taxes are not handled together in the bureaucratic machine (for good reason; individual rights and all that).
The reasons for the complexity are rooted in how the United States is structured politically, where having certain rights and freedoms at each level of governance is a very big deal.