Christian Caryl puts the Egypt/U.S. NGO row in context:

In fact, though, the commentators should have been asking a different question about Abul-Naga — namely, what took her so long. After all, the Americans have been deeply unpopular in Egypt for years. Washington supported Mubarak for decades. Washington is a close friend of Israel. Washington has been invading and occupying Muslim countries. A recent Gallup Poll showed that 70 percent of Egyptians were opposed to further U.S. funding to their country, which they view (without knowing much about the details) as interference in their internal affairs. It shouldn’t really come as a surprise that some enterprising Egyptian politician decided to capitalize on such sentiments.

This touches on something I have talked about before, which is that it is interference itself that is deeply resented more than just the form that interference takes. Even when it is directed towards democracy promotion rather than backing authoritarian governments, the impulse to interfere is still there, and it is still driven by some need to shape and direct the political developments of other nations. For that reason, it generates resentment among people in the country in question, and it doesn’t matter that the purpose of this form of interference is ostensibly well-meaning. If support for authoritarians was justified in the past as a check against communism and then Islamism, now support for opposition forces is justified in terms of making up for having supported authoritarian regimes, but there is always the need to meddle one way or another.

No doubt past and ongoing U.S. support for the Egyptian military regime explains a large part of the opposition to U.S. funding, but the Gallup poll also found that 74% oppose U.S. direct aid to Egyptian civil society groups. That suggests that direct U.S. aid to Egyptian civil society groups will be more of a liability for them with other Egyptians. Given the last thirty years of the U.S.-Egyptian relationship, I’m not surprised that the vast majority of Egyptians does not want to receive “help” from Washington, and opponents of direct aid probably fear that the U.S. is using this aid to try to manipulate and direct how Egyptian politics develops. The common reaction in the U.S. to Egypt’s treatment of IRI, NDI, and similar NGOs has been to tell the Egyptians that they cannot treat these organizations this way without jeopardizing U.S. funding, but according to these Gallup figures most Egyptians want that funding to go away.