Why did David flee from Waknuk in The Chrysalids?
David ran away to the Fringes because one of the Telepaths, Anne, married a normal man and then told him about her special powers. He was the one who turned in David’s friend Sophie, so naturally he was very upset when he learned who he had married. Uncle Axel kills him to protect David, and Anne commits suicide. They find a suicide note, which turns out to be a letter Anne had left for the Inspector.
It denounced all of us, including Rachel herself, and even Petra. It accused us collectively of planning Alan's murder, and one of us, unspecified, of carrying it out. (ch 10)
Anne blames them for her husband’s death. Despite the risk, David thinks things will blow over. They don’t. David and the other Telepaths get a warning to go.
It was a deliberate surprise. If they do know much about us, they'll have tried to time it to send a party for you, too -- before you could I be warned. (ch 12)
The Telepaths flee before they are captured. They are pursued by David’s father and his men all the way into the Fringes until they are rescued by the Sealand people, who are also telepathic.
David and a few other telepaths are forced to flee the Waknuk society because their telepathic abilities have been discovered. That's bad because David's ability is a result of a genetic mutation. Waknuk society views any drastic change to the gene pool as bad and dangerous. As a consequence, the entire Waknuk society watches carefully for any kind of genetic mutation, and the society deals quick and brutal punishments to anybody displaying genetic abnormalities. Those people whose DNA falls outside the "normal" boundary are marked as "Deviants." Being a discovered Deviant forces David to flee because the alternatives are terrible. Now that his secret is known, David risks being banished to the Fringes, being sterilized, or even being killed.
"If the worst comes to the worst, and you can't save Petra, it would be kinder to kill her than let her go to sterilization and banishment to the Fringes—a lot more merciful for a child. You understand? Do the rest of you agree?"
Fleeing Waknuk society is the only real option he has to stay alive and in control of his future.
He left because he was hunted by the group his father controlled, a group dedicated to eradicating any individuals with malformations. His father apparently knew of David's 'gift', and seeked to capture him.
he was found out to be an abomination, the leader of the people who kills these "abominations" was his father and david, his sister and the group fled from being killed