I think this is very likely.
The biggest threat to the current Egyptian government is the terrorist group that is headed by Osama Bin Ladens second in command. Thats the same group that the blind Sheik who we have in jail is involved with. Being a general in the Eyptian Army makes you less, not more likely to be associated with that terrorist group.
You might go on a reprisal against Muslims but most Americans are not going to join you because one idiot does the equivalent of a "drive by" shooting. Now if you had that happening in ten or twenty different airports simulataneously, then you might be right. But not over this. Unless you are a Jew or Israeli or know the individuals involved, its like hearing about the latest drive by or drug killing. Its not going to cause vigalantism.
As far as connection to Egyptian Airlines case. That would be interesting but the only source Ive heard for that was DEBKA, so I doubt that will pan out.
So you tell me, why is the FBI covering up if you feel they are?