When Egyptian President Mohammed Morsi declared it his “duty” to free Omar Abdel Rahman—the man behind the 1993 bombing of the World Trade Center that killed six and injured one thousand—it was not a very auspicious beginning for relations between the United States and the ‘new’ Egypt. The U.S. Congress, particularly the delegation from the New York City area, expressed outrage.

Egypt watchers and Middle East analysts sought to put the new president’s words in context. Morsi is weak. He needs to secure his base and play to public sentiment while he consolidates his power. He does not really intend to pursue Abdel Rahman’s release from U.S. federal prison. Washington would be better served to disregard what was clearly a calculated political move. There are more pressing issues in the U.S.-Egypt relationship than a sick and aging militant.

This sober analysis is entirely accurate, but it sidesteps the central change that has occurred in Egypt since the revolution. Hosni Mubarak could largely ignore public opinion because Egyptian citizens did not have a mechanism for holding their leaders accountable. Now they do. Current and future leaders who disregard public sentiment will do so at their own risk.

The consequence for the United States is likely to be a greatly changed relationship with Egypt. The strategic alignment and the partnership in pursuing Arab-Israeli peace are at best going to get more difficult to manage. At worst, this cooperation will come to an end altogether. Although some analysts are quick to claim that the coming transformation of the U.S.-Egypt relationship is a function of the Muslim Brotherhood’s longstanding anti-American posture, it is more accurately a result of politics and a reflection of Egyptian public opinion. Cairo-Washington ties and the relationship between Mubarak’s Egypt and Israel were profoundly unpopular among Egyptians. In a more open era of Egyptian politics, Washington will discover that over time Cairo will be considerably less willing to support American goals and interests in the Middle East.

The United States (and by extension Israel) have long been important and generally negative factors in Egyptian politics. The January 25 uprising was not about the United States, although it was about national empowerment. For Egyptian revolutionaries, leftists, Islamists, and many liberals, the strategic ties between Washington and Cairo made no sense on both nationalist and strategic grounds. Indeed, the regime that Mubarak led, which had been handed down to him from Anwar Sadat and Gamal Abdel Nasser, was founded in part on opposition to foreign domination.

In addition, as time went by, the Egyptian-American relationship had, in the words of the Muslim Brotherhood’s 2010 electoral platform, “rendered Egypt a secondary power” in a region that it had previously led. Shrewdly, Egypt’s opposition, especially the Brotherhood, used the Cairo-Washington connection to undermine Mubarak’s regime. The burden on Morsi—if he would like to be re-elected—is to demonstrate that he represents a clean break. The fact that the Supreme Council of the Armed Forces (SCAF) gutted the president’s powers through a constitutional decree means that Morsi’s only source of authority is his ability to appeal to the street and subsequently harvest votes. That partly explains his rhetoric on Sheikh Omar Abdul Rahman. The issue will not lead to a breach in relations with the U.S., but it does add a certain amount of tension.

More broadly, Mubarak’s Egypt was a linchpin in a regional political order—that also included Jordan, Morocco, Saudi Arabia, and the small Gulf states—that helped the United States realize its regional and even global interests. It’s unlikely that President Morsi, unlike Mubarak, will order Egypt’s security services to stop and literally take apart a North Korean vessel transiting through the Suez Canal based on an American suspicion that the ship was carrying missiles destined for Syria. Whereas Mubarak seemed willing—albeit with a measure of reluctance and public protestation—to do America’s bidding, Morsi simply cannot. He has to be a better nationalist, a better steward of Egypt’s interests, and more mindful of Egypt’s place in the Middle East. If he is not, Morsi will become a short-lived local experiment in Islamist power and be replaced by someone who can approximate the deeply held ideals and aspirations of the newly empowered Egyptian electorate.

President Barack Obama and his administration handled the Egyptian uprising about as well as could be expected. What was happening on the streets of Egypt during those eighteen days in early 2011 was unprecedented. To be sure, Egypt has seen mass protests before but, with the exception of a brief moment during the 1977 bread riots, the regime’s durability never seemed in doubt. From the very start, the January 25 protests seemed different, which is why the accusation that Obama “lost Egypt” is so misplaced. The United States had no way of altering the trajectory of events once the uprising began. It was impossible to “save Mubarak”—as valuable an ally as he may have been over the previous thirty years—without encouraging massive bloodshed. This was not something that Obama was prepared to do. So, the United States threw its support behind those who want to live in a more democratic society.

Until Morsi’s election in June, U.S. policy was more an aspiration—the development of a democratic Egypt—than an actual policy. To the extent that Washington has a policy toward a more democratic Egypt, it is to engage, adjust, and hope that its interests—over-flight rights, expedited transit through the Suez Canal and other security-related logistical support, and peace along the Egyptian-Israeli frontier—will remain intact.

It is unclear how the United States will go about securing these interests. U.S. policy has been predicated on a deal with President Mubarak and the Egyptian military that conflicted with Washington’s stated desire to see democracy take root on the banks of the Nile. If Washington pursues a similar approach where it relies on the military to help achieve its goals, this contradiction will once again make the United States an important, but essentially negative, factor in Egyptian politics. In the short run, SCAF is intent on maintaining its autonomy and seems willing to continue to accept U.S. aid, but that does not mean that Washington has leverage over the generals. Washington needs them as much as the Egyptian Ministry of Defense needs the Pentagon.

Indeed, assistance—both military and economic—cuts both ways for the United States. Washington’s annual $1.3 billion aid package does appear to have some influence over important players at critical moments, but it is largely a negative factor, and will likely have diminishing returns in a more democratic Egypt. In addition, the U.S. Congress is wary of both the Muslim Brotherhood and SCAF. This will almost certainly result in a bruising battle on Capitol Hill about the future of the aid—something most Egyptians seem to be ambivalent about, anyway.

As much as official Washington hopes it can muddle through Egypt’s prolonged transition with its interests intact, the American position in Egypt will change and it will wane. And any side deal–which would have the elected civilian government tending to domestic issues while Egypt’s generals ensure U.S. strategic interests—will prove unsustainable. Washington must fully come to terms with a new and perhaps democratic Egypt.

Steven A. Cook is the Hasib J. Sabbagh Senior Fellow for Middle East Studies at the Council on Foreign Relations, where he publishes the blog “From the Potomac to the Euphrates.” He has written for Foreign Affairs, Foreign Policy, the New York Times, Washington Post, Wall Street Journal, and Financial Times. His most recent book is The Struggle for Egypt: From Nasser to Tahrir Square. He can be followed on Twitter at @stevenacook.