Since the Camp David Accords between Egypt and Israel in 1978, the United States has sent annual military aid to both countries as part of the agreement. Egypt has received about $1.3 billion a year in military aid (and a smaller amount in "economic aid") since 1979. The Camp David Accords helped set the stage for the assassination of Egyptian President Anwar Sadat by Islamic fundamentalists in 1981; he was succeeded by Hosni Mubarak. As the Mubarak regime built on the authoritarian legacy of Sadat and his predecessor, Gamal Nasser, U.S. aid continued, the bulk of it to the military apparatus that allowed Mubarak to retain power, and which was understood by the U.S. to be the underpinning of the Egyptian state.
No Amnesty International report on the human rights abuses perpetrated by the Egyptian state was going to jeopardize military aid the U.S. believed to be crucial to maintaining "stability" (pdf) in the region. It was the military that finally helped push Hosni Mubarak out of power in 2011 during mass protests in Tahrir Square. Military aid from the U.S. continued through the transition and after Mohamed Morsi was elected. Aid continued even as Obama said Egypt wasn't an ally anymore (the State Department quickly corrected him), and survived sporadic efforts to cut it as the regime in Egypt became less openly pro-American.
Since the weekend, Egypt has been gripped by protests even larger than the 2011 protests that saw the ouster of Mubarak. The military eventually issued an ultimatum, threatening to intervene if what they perceived as the demands of the people were not met. When the deadline passed, the military stepped in, ousting Morsi and suspending the Constitution he pushed through with a snap referendum last December. While the generals appeared to be backed by some of the most important religious figures in Egypt (the Grand Imam of Al-Azhar University and the Pope of the Coptic Church) as well as Mohammed ElBaradei, a leading secular figure in the opposition, the military also reportedly shut down Islamist-run TV stations.
Now, for probably the first time in more than thirty years, the U.S. says its actually reviewing its military aid to Egypt (it set conditions before, but the aid's always eventually come) based on a rule requiring suspension of aid following a military coup (except when that doesn't suit Washington's interest, like in Honduras). The U.S. government is highly likely to decide the coup in Egypt wasn't really a coup and find a way to keep the aid flowing. Even though Egyptians on the street appeared to blame the Obama Administration for supporting the Muslim Brotherhood government, much of the U.S. aid during Morsi's rule continued to go to the military. And that's the problem.
As Shikha Dalmia rightly noted last summer, U.S. military aid to Egypt has contributed a lot to the dire economic situation in Egypt because it's allowed the military to secure and maintain a stranglehold on the Egyptian economy. Economic woes played a large part in the series of Mubarak era food riots and protests that eventually led to his ouster, and were a major factor in the current round of protests. As I wrote earlier this week, so long as Egyptians (or any protesters) expect more government intervention to fix the economic problems caused by government intervention there isn't going to be a happy ending. The U.S. cutting military aid, then, might do more to set Egypt on a path to stability than any amount of U.S. military aid would.