The future of Zahi Hawass, a Mubarak loyalist, is being openly discussed. See
http://news.sciencemag.org/scienceinsider/2011/02/after-the-revolution-who-will-co.html
According to Twitter, a demonstration is being scheduled to demand his ouster. See
http://www.google.com/search?q=zahi+hawass&hl=en&sa=G&prmd=ivnsuofd&tbs=mbl:1&tbo=u&ei=nc1XTaWxGcK78gbX2qSKBw&oi=realtime_result_group_more_results_link&ct=title&resnum=4&ved=0CDoQ5QUwAw
Addendum: Dorothy King (PhDiva) has replaced a report on her blog that alleges that monies from the Museum and travelling shows have been skimmed off over the years. See http://phdiva.blogspot.com/2011/02/problems-with-sca-in-egypt.html