The funding of most federal agencies is actually a two-step process. First, Congress must authorize the creation and continuation of the agency and define how it will be funded. Authorization can also set agency organization, programs, and spending limits. Authorization is usually for a fixed period of years.
Then each year, Congress must appropriate money for the agency to operate for the fiscal year (October 1 to September 30). The president submits to Congress his recommendations for appropriations each year, and this is commonly referred to as the budget.
Authorizations and appropriations are handled by different committees in Congress. Both the "authorizers" and the "appropriators" can profoundly affect how a federal agency operates but by using different legislative tools.
The FAA submitted its appropriations request for fiscal year 2008 to the president, and in turn submitted his appropriations requests for all of the government to Congress in February.
But remember, even though the FAA is asking for money for 2008, it hasn't yet been authorized to spend it, nor for that matter, has the agency even been authorized to continue existing.
So the FAA wrote its own version of its authorizing legislation and submitted it to the Department of Transportation. It was vetted, edited, and altered to reflect the department's priorities. From there, the White House Office of Management and Budget reviewed it and changed items to reflect its own priorities and political concerns.
The administration submitted its proposed FAA funding measure, technically called the FAA reauthorization bill, to Congress, calling it the Next Generation Air Transportation System Financing Reform Act of 2007. The bill proposes increasing the general aviation gasoline tax to 70.1 cents per gallon, charging GA user fees for operations in Class B airspace, and increasing or adding fees for FAA services such as pilot certificate issuance. Meanwhile, the bill would eliminate taxes for the airlines and charge them user fees instead, reducing the amount they pay for FAA operations by up to 27%.
Now the relevant House and Senate committees are considering the issue. They may choose to accept the proposal, change it, or write their own.
Typically, at the end of this process the U.S. Congress authorizes the FAA to spend its annual budget and tells the agency how it can divide the money among four main areas of responsibility: airport improvements, air traffic control enhancements, FAA operations, and research and development.