What methods of control (physical, psychological, or otherwise) are applied by the leaders in Anthem by Ayn Rand to ensure minimal resistance from the citizenry? How does Rand use this to communicate greater truths (either about her philosophy or about humanity in general)?

In Ayn Rand's dystopia, collectivity is ruthlessly enforced and individuality is vigorously suppressed. This repression begins at birth, when babies are placed into collective nurseries. In school, while there is some attention to students' talents, excellence is largely suppressed, and originality is thwarted. When children mature, their Life Mandate, or employment path, is decided for them by the Council of Vocations. The selection criteria are what is best for society, regardless of personal preference (which would be a Transgression).
If the originality has not been sufficiently squashed and the worker complains or slacks off, they can be subjected to corporal punishment and/or sent to the Palace of Corrective Detention. This decrepit old prison is too derelict to keep anyone from escaping; but no one tries to escape, because either they are afraid of the forest outside or they lack the initiative to try anything daring.
Ayn Rand was originally Russian, but she moved to the United States when she was twenty-one. She was disturbed by many developments in the Soviet Union, especially Stalinism. Rand became an ardent laissez-faire capitalist, promoting a far right political philosophy—what today is called libertarianism—that opposed all social welfare programs and championed unrestricted individualism.