We study aspects of the pion condensation in two-flavor neutral quark matter using the Nambu--Jona-Lasinio model of QCD at finite density. We investigate the role of electric charge neutrality, and explicit symmetry breaking via quark mass, both of which control the onset of the charged pion $(pi^c)$ condensation. We show that the equality between the electric chemical potential and the in-medium pion mass, $mu_{e}=M_{pi^-}$, as a threshold, persists even for a composite pion system in the medium, provided the transition to the pion condensed phase is of the second order. Moreover, we find that the pion condensate in neutral quark matter is extremely fragile to the symmetry breaking effect via a current quark mass $m$, and is ruled out for $m$ larger than the order of 10 keV.