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This is happening despite promises by Tantawi, head of SCAF, that civilians won't be tried in military courts. It has become the rule that SCAF doesn't fulfil its promises.
There is hardly a wall in Cairo (perhaps in the entire country) that isn't covered in graffiti, this was never the case before the revolution. The statement 'down with military rule' covers lots of walls these days. However, Aly was spraying a Graffiti warning people against the remnants of the old regime.
UPDATE: He was released after paying a hefty fine and a week in jail.