Clinton Dan McKinnon, President Reagan's choice to be chairman of the Civil Aeronautics Board, breezed through Senate hearings yesterday on his nomination to oversee the agency during its waning years.

The board, which has regulated air transportation since 1938, is scheduled to go out of existence on Jan. 1, 1985, unless Congress alters the schedule set by the Airline Deregulation Act of 1978. The CAB loses authority over airline entry to domestic routes at the end of this year and authority over domestic fares at the end of 1982.

In a half-hour hearing before the Senate Commerce Committee yesterday, McKinnon said he believes in airline deregulation and thinks it has accelerated enough to permit the board to begin phasing out some of its activities before the final "lights out."

Sen. Howard Cannon (D-Nev.), a chief sponsor of airline deregulation, asked McKinnon about the wisdom of allowing airlines fare flexibility at a time when entry to new routes--a cornerstone of deregulation--is being crippled at major airports by the Federal Aviation Administration because of the air traffic controllers strike. "That's a good question," McKinnon responded, promising to "work with the FAA to assure that all airlines have fair access to the 22 regulated airports."

Not surprisingly, McKinnon told the committee he shares the same philosophy as President Reagan, whose campaign for president he contributed to. But he said that he does not feel bound to support administration positions on issues that may come before the board. "It's my understanding that the CAB is an independent regulatory agency, and if you're part of an independent regulatory agency, you need to have independent thinking . . ." he said.

McKinnon, 47, is the owner and operator of two country music radio stations in San Diego and is a part-owner with his brother of two television stations in Corpus Christi and Beaumont, Tex. He also owns the House of Hits Music Publishing firm.

A former Navy pilot, McKinnon holds the record for the rescue of 62 lives as a Navy helicopter pilot.

The son of a former congressman, McKinnon ran unsuccessfully for a seat in Congress in the California Republican primary last year, losing to Rep. Bill Lowery (R-Calif.), who introduced him to the committee yesterday.