people who don't understand why they didn't run...
are brainwashed. There's no other explanation for your lack of realization that childhood indoctrination is one of the most powerful determinants of who you are as a person. They were raised told they were different, with strict rules dictating their behavior 24/7, eliminating any semblance of individuality. They were even made aware of their purpose, and the way they say "complete" with no knowledge that it's a disgusting euphemism suggests they consider what they're doing to maybe even be noble.
Barring all that, what the hell do you expect them to do after they've escaped? Join the system, start a business and live happily ever after? They didn't know anything about the world, they had zero identification or record they exist anywhere other than clone facilities. Coupled with the fact the corporation that made them wouldn't be too thrilled about escapees ruining potential future business.
Anyway, a recurring principle in greedy elites who put people situations like this, is they know FORCING people to work for your interests against their own always comes with risk of revolt. But, if they convince the victim their interests coincide with the "master's", they get a much more reliable result. That could even be one of the comments the movie makes, about how our society HAS become a bunch of followers, working against our interests, when the gate to our freedom is right in front of us.