When Todd takes Jesse out from his cage to 'help' him dispose the dead body of his cleaning lady out in the desert, Jesse gets a golden opportunity to kill Todd when he gets hold of his gun. Jesse always hated Todd right from the point when he shot the kid in the desert to him being caged and then killing Andrea. Keeping all that aside, it would make perfect sense to kill Todd just for his own freedom. Also, there were no witnesses out there in the desert. It was a perfect escape.
But he doesn't kill him and instead settles in for a pizza and cold beer on the ride back to his cage. Why in the name of good God would Jesse do that?
Initially, I thought it must be inertia; that Jesse is too used to his caged lifestyle that he doesn't like the idea of freedom; that the cage is now his reality; that he has made peace with it and with Todd. But later in the timeline of Breaking Bad, he actually does kill Todd by choking him to death and fleeing in the car roaring his freedom. What changed after? Why did he choose a pizza and beer instead of his freedom?