In A Clockwork Orange, the Government seeks to suppress individuals and individual choice in favor of the stability of the State, largely to ensure its own survival. Towards this end, the Government is prepared to do anything necessary, including distributing propaganda and censorship, employing morally questionable scientific techniques to "reform" criminals, and employing criminals as state patrol to threaten other citizens (and potential political dissidents).
From its treatment of Alex, one can clearly gauge how the Government is willing to sacrifice the individual liberties of its constituents for the stability of the State.
The Government is the chief antagonistic force against Alex in A Clockwork Orange, because of the differing views it espouses on the subjects of morality, personal liberty, and freedom of choice.