Fear is one of the dominant themes of The Chrysalids. Explain how this theme motivates the main characters throughout the novel.

You are correct. Fear is a constant theme and motivator for characters in the novel.  The fear is a real fear too.  The Waknuk society doesn't tolerate any kind of genetic abnormalities.  If any kind of unacceptable genetic mutation happens, that person is either killed or expelled from the society entirely.  Because of those fears, Sophie's family keeps her 6 toes a secret from everybody.  David doesn't understand why he must keep it a secret at first.  He does eventually come to understand why Sophie and her family are afraid.  David is put into the same kind of fear and situation when he learns that he is a telepath.  

David isn't the only telepath, and the entire group lives in fear of being found out.  That fear comes to a tipping point in chapter ten.  Anne, a telepath, plans to marry.  The rest of the group fears that her secret will be discovered with her marriage, and in turn the rest of the group will be found out.  Out of fear for David's safety, his Uncle Axel kills Anne's future husband.  

In chapter twelve, two of the telepaths are captured.  The rest of the group is fearful that they will be discovered, so they flee the Waknuk society together.  They figure living on the run is better than being killed.  From this point forward, the telepaths are on the run from the Waknuks and the people who live in the Fringes.   Everything they do is focused on reaching the "Sealand" people who might offer some kind of unknown sanctuary.