I think the Egyptian military liked the status they enjoyed under Mubarak far more than the one they inherited (and that we pushed for in demanding that Mubarak step down).

They don't want to be in charge, but they don't want to end up in a position worse than what they once enjoyed.

As Dayuhan points out, these things are complicated. When dictators fall it is almost always far more the end of the beginning, rather than the beginning of the end.