WASHINGTON—It is becoming apparent by the day that the wrong people are winning and the right people are losing in Egypt.

Hosni Mubarak had indicated he would not seek re-election long before the uprising, which is why he was grooming possible heirs. The standard by which to judge how he comes out of this trying period, therefore, is not whether he remains in power. It is whether the political structure that has dominated the country will survive.

Circumstances occasionally forced Mubarak to make temporary concessions during his three decades of autocratic rule. In 2005, for instance, the Muslim Brotherhood participated in elections under several restrictions. The regime, a mercantilistic tangle of military, political and business interests, was skillful at blackmailing the outside world into believing that dictatorship was necessary. A cable sent that year by U.S. Ambassador Francis Ricciardone to FBI Director Robert Mueller, in preparation for the latter’s visit to Cairo states that Egypt’s authorities have “a long history of threatening us with the MB bogeyman.” Ricciardone warned Mueller that Cairo would blame Washington’s pressure for the success of the Islamists in the elections—and suggested that Mueller reply that it was precisely the lack of democracy and transparency that was fueling extremism.

The Islamist cover allowed Mubarak and company to build a veritable empire of corruption. Unlike in Cuba, where foreigners cannot own a majority stake in any venture, in Egypt they are obliged to cede just one-fifth of the ownership to local partners. But these local partnerships almost invariably lead to the presidential palace or the military. A book by Aladdin Elaasar titled “The Last Pharaoh” and an in-depth investigation by the newspaper Al Khabar offer detailed accounts of the billions of dollars that Mubarak and his family have in Egypt, where they own property along the Red Sea, as well as in Britain and Switzerland.

A transition presided over by Mubarak, negotiated by his longtime spymaster and now Vice President Omar Suleiman, and controlled by the same army that made sure, with Machiavellian cunning, that people could vent their anger in Tahrir Square without ever putting in danger the presidency of the boss, is bound to produce an election that will preserve a lot more of the regime than will be changed.

Paradoxically, this does not mean that Mubarak’s main foe, the Muslim Brotherhood, has lost. They are also winners at this point. Their goal has never been, during the uprising, to take over power. They have behaved with an acute sense of the long term. They kept quiet for days, watching. Only when they confirmed the extent of the revolt did they step, sheepishly, forward. Even then they proposed Nobel laureate Mohammed ElBaradei as the frontman of the resistance while accepting the need for a larger committee of secular representatives. At no point did they initiate any violence. They waited until Mubarak unleashed a horde of gangsters on the protesters, then mingled with young Egyptians fighting for change and resisted the assault: Mubarak’s men were never able to dislodge the protesters from Tahrir Square, no matter how much blood was spilled and how many foreign witnesses brutally removed.

Ordinary opponents of Mubarak would have to be inhuman not to quietly admire the bravery with which the crowd, including the Muslim Brotherhood, repelled the armed onslaught.

And now the Muslim Brotherhood has done something intelligent: It is taking part in negotiations with Suleiman that likely will not change anything substantive in the short run but might open up a few little spaces for the Brotherhood to continue its long march to power. How long? It doesn’t matter one bit. The Brotherhood was founded in 1928 and almost a century later is the only organization in the Middle East with popular roots, an extensive network of social aid, and spiritual ascendancy over millions who have not found any civilian alternatives because, in a region where your choices are to be an autocrat’s minion, a terrorist or a civil non-entity, none have been allowed to blossom.

Who loses in this scenario? The same people who have been losing for decades—the aspiring leaders desperate to prove that the choice is not between tyranny and Islamic terrorism but between obscurantism and civilization, and the millions whose hearts must be heavy with frustration at watching the turn of events.