As I've mentioned here before, Vito seems a textbook case of Post-Traumatic Stress Disorder. The childhood experience revolving around his father's death and his flight from Sicily very likely triggered Vito's response to Fanucci, with Fanucci standing in the place of Don Ciccio as the person who would not leave Vito alone. What Fanucci saw as a little shakedown, Vito saw as a death struggle.