What is David's main goal in The Chrysalids?I know that he tries to keep his thought-shapes a secret, and has to try to keep himself alive, but his main goal...?
Actually, you are completely right. As the story develops, his goal does change accordingly, but you have identified his raison d'etre for the first section of the novel. It is clear that when he tells his Uncle Axel about his "gift" and Uncle Axel insists that he and the others never reveal or talk about their abilities to anyone, that David's goal is safety and ensuring that no one discovers about the group:
It changed our lives by marking our first step in corporate self-preservation, though we understood little of that at the time.
Of course, this "self-preservation" is threatened by a number of events, first Ann getting married, and then with Petra arriving. However, you could argue that David's goal changes somewhat when he is given the mission of fleeing with Petra and preserving her at all costs. David of course wants to protect his lover, Rosalind, and his sister, Petra, from the future that his friend, Sophie faced when she was discovered. Also, they know what has happened to Katherine and Sally and are terrified of the kind of torture that would await them upon discovery. Therefore fleeing and reaching the Fringes becomes vital.