To me, the answer has been clear for two weeks or so and more so in the last week, when Tantawy's reassuring words in a cabinet meeting were followed by the launching of an extremely aggressive state media campaign led by al-Ahram. And guess what is supposed to have happened today: the editor of al-Ahram was replaced.
The state media in Egypt has been fragmented, but state television and major organs like al-Ahram have long been the province of General Intelligence. Their men ran these places, and perhaps they still do.
The only logical alternative explanation would be that SCAF is consciously playing a good cop-bad cop routine where they set themselves up as the nice guys but point to bad guys (and public opinion, and the Brothers) who can be much more trouble than just dealing with the military.
The other interesting point here is that senior US officials have discreetly made the rounds in Washington in the last week saying that SCAF was not responsible for the crisis (which may be to protect SCAF from Congress, but is still telling.) More likely in my opinion is that this is partly true, and we are dealing with a fragmented regime today much as we were in the last years of the Mubarak era. Or a mixture of both good cop/bad cop and inner-regime intrigues.
The FT puts it well here:
Some analysts, however, argue that there is more to the argument than distraction, suggesting that forces in the unreformed security services that underpinned the Mubarak regime could be laying the ground for an attempt to torpedo the country’s political transition.
“I am hearing assertions that the military council does not want this fierce [anti-American] campaign,” said Ezzedine Choukri Fishere, a former Egyptian diplomat and an analyst. “This is something that is organised but within a more general situation of chaos ... The army and the council care about the military aid, but not so the security services.”
Especially if the security services are worried that SCAF will sell them out to the incoming civilians to win their own immunity.
Games, and games within games. If this goes on Egypt's politics will start to resemble Algeria's.