The scientists realized and acknowledged the creation of nuclear bombs and how much destruction they could cause so they created a secret city to keep the population alive and protected from these bombs. (i know this from reading the third book)
It probably had something to do with the fact that the earth wasn't really great to live on when Ember was created. Even though when the book takes place Ember was having a hard time supporting life (flickering lights, more blackouts, little known food), it was a better option than living on the Earth was, at the time.
