The Speaker of the House is not second in line of Presidential succession. The second in line would be the Vice President. Then it would be Speak of the House; who is currently Paul Ryan.
The reason this happened boils down to favoritism within the Truman presidency. He proposed to change the succession in 1947 because he preferred the Speaker of the House who at the current time was Sam Rayburn over the President Pro Tempore of the Senate, Ken McKellar.