I’m pretty protestors want the military rulers to resign and may be ambivalent towards the civilian Cabinet.
The military-civilian crony capitalism regime of Egypt didn’t go away when Mubarak resigned. If these protests move to seek removal of military rule itself, then it is truly demanding a new power structure in Egypt, and it makes sense that the generals are less willing to toss themselves out then they were for tossing Mubarak.
UPDATE: Damnit I just crossed into the usual speculative punditry. I suck.