This is an article about allegations that the military used the museum for interrogating and possibly torturing people they arrested in Tahrir Square during the revolution but there are also sections discussing the status of the museum in the eyes of Egyptians following these alleged events. There is also an interesting mention of multiple break-ins by looters, one/some after February 11th. Here's an excerpt:
Despite the testimonies of Sobhy and others, many refuse to believe that the armed forces are perpetuating the human rights abuses of the previous regime by imprisoning, torturing and humiliating protesters within the walls of the nation’s most prominent cultural landmark. But regardless of the extent of brutality allegedly taking place on its grounds, there is little doubt that the role of the Egyptian Museum has significantly shifted during the revolution, in a way that mirrors the complicated and at times contradictory nature of the current Egyptian situation.
“The museum is clearly very valuable, and precious, to the Egyptian people,” said Fayza Haikal, a professor of Egyptology at the American University in Cairo. This value, though, is double-edged. Immediately following the withdrawal of police forces, the museum was seen as a jackpot for looters, whose pilfering was largely prevented by a brigade of volunteer civilians forming a human shield around the building.
“The museum was looted more than once, especially after 28 January and 11 February. Luckily, most of what was stolen was retrieved, and all that remains missing is a few smaller artifacts," Haikal said.
“The fact that civilians took it upon themselves to defend the museum from looters is an indication of how valuable it is to Egyptians. Both in terms of our historic wealth, and as a cultural icon."
Haikal seems to be among a minority who do not think the museum’s status as a “symbol of the Egyptian people” will suffer in the face of allegations that the institution is currently doubling as a “torture camp.”