We investigate the transport properties of open quantum chaotic systems in the semiclassical limit. We show how the transmission spectrum, the conductance fluctuations, and their correlations are influenced by the underlying chaotic classical dynamics, and result from the separation of the quantum phase space into a stochastic and a deterministic phase. Consequently, sample-to-sample conductance fluctuations lose their universality, while the persistence of a finite stochastic phase protects the universality of conductance fluctuations under variation of a quantum parameter.