A rare article looking at this relationship by Robert Springborg, a NPS professor:http://www.egyptindependent.com/opin...-officers-club

Taster:
In sum, Morsy and his colleagues in the Brotherhood are putting their newly established relationship with the military to a real test. Presumably, their assumption is that they can count on the loyalty of senior military personnel out of shared Islamist thinking, combined with solicitousness of the military’s institutional interests.

But this assumption could be incorrect. Four months may not be long enough for the new military leadership to have cohered into a like-minded group dedicated to the preservation of the Morsy government, to say nothing of establishing the networks of loyalty and control down into the army.

And while that government has demonstrated extreme sensitivity to the military’s institutional interests, its grab for power threatens the very nation and its unity that the military sees as its primary role in defending.