This piece by Noha Hennawy in Egypt Independent has it right — it's not about Brotherhood vs. military in Egypt, it's not even Brotherhood vs. the military and the judiciary, it's about Brotherhood vs. military and a range of potential allies, some of whom are only allies on occasion:
In the midst of this feud, the Brotherhood and its political wing, the Freedom and Justice Party, have also immersed themselves into a different battle with another, no less significant force: privately owned media. The group’s daily newspaper recently coined the term, ‘black media’, for the private channels and newspapers that regularly criticize the Brotherhood’s performance. It accused these media outlets of implementing the agenda of corrupt businessmen, known for ties with the old regime.
Akram Ismail, a columnist and youth leader in the leftist Popular Alliance Party, says the Brothers may not win these battles because their adversaries ‘are very powerful.’
‘The Brothers are fighting influential groups,’ he said, listing the bureaucracy, the businessmen, the upper-middle class, intelligence officials and the security apparatus.
‘It is a large social mix,’ he said. ‘The Supreme Council of the Armed Forces stands as the political representative of this network.
‘These forces might not be able to form a political party and win elections, but they can invest in the media, the military council and the judiciary to team up against the Brotherhood,’ said Ismail, addressing what is commonly referred to as ‘the deep state.’"