This New York Times article is portraying Egypt's Minister of Planning and International Cooperation Fayza Abu'l-Naga's campaign against foreign NGOs as being carried out in defiance even of the Military Council. In this view, authority is increasingly divided and the Minister appears to be alienating the US without the approval of SCAF. I am, frankly, skeptical.
I know SCAF has shown plenty of signs of disorganization, internal division, and incompetence, but that doesn't mean it's powerless. If the Minister of International Cooperation can alienate a key ally/aid donor unilaterally, why has every other Minister in the Cabinet, including Prime Minister Ganzouri, seemed to ask SCAF's permission before every statement? Admittedly, the alternative — that SCAF itself is behind the campaign against NGOs — requires assuming a level of Machiavellian scheming (pledging good relations when Field Marshal Tantawi meets General Dempsey, while pursuing the NGOs at the same time) that raises plenty of questions, too.
I think the NYT article could be the correct reading, but I frankly doubt it. I'd guess (and it is just a guess) that SCAF is gambling that it can play the popular "foreign interference" card domestically (and remove annoying democracy activists in the process) without losing the US aid package, calculating that the US military values the strategic relationship too much to jeopardize it. I suspect that may in fact be true of some in the US military, but they don't make US policy in an election year, a factor SCAF may be badly underestimating.
On the other hand, I can easily imagine the generals leaking to the NYT the "fact" that they just can't control this rogue crazy woman in the Planning Ministry, so don't blame them for what's happening, blame her. But again, I'm not there; I'm going on experience and instinct, and could be wrong.