The tail section is upward for clearance or to vector up the engine exhaust that will help to rise the nose when the aircraft take-off?
Quoting from the Design section of the Wikipedia article on the F-104:
The aft fuselage was elevated from the horizontal reference plane, resulting a "lifted" tail, and the nose was "drooped". This caused the aircraft to fly nose up, helping to minimize drag. As a result, the pitot tube, air inlet scoops, and engine thrust line were all canted slightly from centerline of the fuselage.