Although Egypt's Supreme Council of the Armed Forces has said it would avoid trying civilians in military court "except for violations of military law," in fact civilians have continued to appear in military courts since the revolution. The recent arrest of blogger/activist Alaa Abdel Fattah appears to be turning into a cause celébre for those opposed to SCAF and military courts. Summoned for questioning on suspicion of "incitement" in the violence at Maspero on October 9, he returned to Egypt after a visit to California and then refused to answer questions of the military prosecutor, on the grounds that 1) since he is a civilian they have no jurisdiction and 2) since military police were involved in the Maspero clashes a military prosecutor should not be investigating the incident.
Abdel Fattah, who founded a well-known aggregator blog with his wife Manal (most posts are in Arabic), and is a vocal presence on Twitter (@alaa), has provoked a lot of sympathy, and growing protests in Egypt and Tunisia as well as in the online community.
If I had to guess, I'd wager that SCAF will let him go within the 15-day detention period since he has become such a high-profile figure. But I think he would remind them that there are thousands of Egyptian civilians detained by military prosecutors who have no international profile or support base.