You really don't have to be too concerned about the problems in Cairo. The press blows everything out of proportion. The protest area is relatively confined to a small area and the tourist sites, hotels, and museum areas are unaffected by it all. Clients of ours who have been there say they were glad they went because they were treated royally. Personally, I would not hesitate to go - just have to stay within the tourist areas and it's fine.
We were in Athens when they were having problems and it, too, was confined to a certain area. The press made it seem like the whole city was under siege and that couldn't be further from the truth. We were glad we went, had a great time, and our cab driver just made sure to take us around the affected area and we had no problems whatsoever.
Our next big trip we would love to go to Cairo and Jordan, then take a river cruise down the Nile. If we had the money, we would do it right now without hesitation.
On another note, if you want to see Turkey, you really ought to see Croatia - it truly is a wonderful place to visit and Dubrovnik was absolutely an undiscovered jewel. Split was amazing and a very historic place.
We spent 14 nights doing a cruise in the area and it was incredible. There are some awesome places to visit.