Liberal and Christian politicians and public figures have condemned US Secretary of State Hillary Clinton’s visit to Egypt, accusing the administration of President Barack Obama of harbouring bias in favour of Egypt’s Islamist parties, especially the Muslim Brotherhood.

It is an ironic charge. One could have never imagined even last year that Washington could have a pro-Brotherhood bias. The gap between them is too wide to be bridged in a hurry.

The case of Egypt is unique. On the one hand is the country’s powerful military, which has usurped for itself all legislative and executive powers. By virtue of having retained the ousted Mubarak regime’s judges, the ruling generals are also in control of the country’s judiciary, and they are refusing to deliver on their promise to hand over power to an elected civilian government.

Clearly, the military’s policies and actions negate the very grain of democracy that the US says it wants to promote in post-Mubarak Egypt. At the same time, the Obama administration cannot afford to challenge the military (not that it wishes to do so), given that the armed forces are the best guarantors of law and order in the country and they are already in control.

Therefore, it is inevitable that Washington has to deal with the ruling generals while scaling down calls for an early end to their rule.

On the other hand, the Muslim Brotherhood is the democratic choice of the Egyptian people, as we saw in post-Mubarak parliamentary and presidential elections. But the group does not have legislative or executive power, with the military having disbanded the post-Mubarak parliament and deprived the president, a Muslim Brotherhood leader, of any real authority.

The Brotherhood is accused of pursuing an Islamist agenda and wants absolute power for itself, which, critics say, will be used to impose the group’s will on the country and people.

Liberal parties and movements accuse Washington of interfering in the internal affairs of Egypt and having made a deal with the Muslim Brotherhood.

Indeed, the accusations are Israel centric, with the activists saying that the US agreed to having Mohammed Mursi as president in return for Egypt ensuring Israel’s security by pressuring Hamas – the Brotherhood’s branch in Palestine – not to launch military attacks against Israel and even accept the Camp David peace accord with Tel Aviv.

Under the alleged agreement with the US, the Brotherhood is also expected to maintain Mubarak-era agreements not to restore ties with Iran.

It is highly unlikely that such an agreement exists, but the two sides know what each other wants and both can play the game. So does the military.

It is also highly unlikely that Clinton tried to apply pressure on the ruling generals to hand executive power over to the Muslim Brotherhood, as liberals, seculars and Christians are claiming. Simply, it is not in US interests to have a Muslim Brotherhood man as a powerful president of Egypt.