The saliva from fleas is the primary cause of the skin itching after being the victim of a flea bite, and not the actual bite its self. The flea injects a numbing agent or minor anesthetic when latching on to the skin in order to avoid being detected, which can also be responsible for skin being itchy.
The saliva from fleas can also contain many different kinds of bacteria and germs, and even some diseases. Such things can also cause the skin to become irritated and itchy. It is important that a flea bite not be scratched as the human fingernails also carry plenty of bacteria that, when introduced into the bite in the form of scratching, can also cause more irritation and itchiness.