If you're asking why Sonny said, "He's not your father," well, Vito wasn't Tom's father. But more to the point: Sonny wasn't very sensitive (later he hurls at Tom, "Pop had Genco, look what I got"). He may also have been expressing resentment toward Tom for advocating negotiation rather than shooting. Sonny also may have been feeling guilty because he knew that his gaffe at the Solozzo meeting triggered the attack on his father. Sonny would feel less guilty if he killed Sol rather than negotiate with him.