This is an excellent inquiry into the puzzling developments in the recent conflicts about NGO operations in Egypt between Egyptian's military ruling class and US officials. The author raises some important questions about NGOs, their sponsors, and their operations in foreign countries. Much has already been written about the Empire's use of NGOs to engineer the "color revolutions" (see this and this) in various countries, and also the use of non-profit organizations (NGOs are just non-profits operating abroad) extensively here in the US, the center of the Empire, to guide public opinion behind policies that are consistent with those of the ruling class (see this and this).
One can easily conclude that NGOs are used as a Trojan horse to shape policies in foreign countries to suit the ruling class of the Empire. In other words as the author suggests, many existing NGOs should be designated as IGOs (informal governmental organizations).
The author also tries to untangle the real motives behind this puzzling conflict between the two parties--the officials of the Empire and officials of the client state.
...the protests from Washington and the media assessments of the controversy seem willfully misleading. Since when does Washington become so agitated on behalf of NGOs under attack in a foreign country? Even mainstream eyebrows should have been raised sky high when Martin Demsey, currently the Chairman of the Joint Chiefs, while visiting Cairo was reported to have interceded with his military counterparts on behalf of these Americans made subject to a travel ban and faced with the threat of prosecution. When was the last time you can recall an American military commander interceding on behalf of a genuine NGO? To paraphrase Bob Dylan, ‘the answer my friends, is never.’ So even the most naïve among us should be asking ‘what is really going on here?’