At bottom, the idea of state autonomy refers to a capacity of the state to act independently of social forces (particularly economic forces). This does not mean society is irrelevant.
It just means that an arrangement of social forces does not uniquely determine particular state actions.
Marxists such as Poulantzas speak of the "relative autonomy" of the state.
Pluralists at least theoretically allow for state autonomy when the "vector of group pressure" is unclear (that is, when the pressures generated by social groups do not result in clear political demands). And of course state autonomy has been a central concern of statist theorists such as Krasner and Skocpol.
The predominant conception of state autonomy revolves around the idea of freedom from external (societal) causal influences. This idea goes as follows. If system x (say a state structure) is autonomous, it is not driven completely by forces outside of itself.
Autonomy means _________________________; that is, the system has a set of boundaries.
1.state-governing territory
2.self-contained causality
3.economically-defined concept
4.politically-independent system
5.passively-protected independence