DO NOT try doing Egypt on your own. Half the people in that country live in homes with dirt floors. It is very poor and sanitation is not good at all.
Never eat in a restaurant that is not 4 star hotel or equivalent. Never eat street food or drink liquids that are in bottles already opened. Never drink tap water. Also, for security, when you take a taxi, take it from your hotel and have the hotel register the taxi driver.
Tours are the way to go. DO NOT drive in Egypt, I have visited that country twice. You have no idea how aggressive the locals drive. The infrastructure is not very good and traffic is terrible.
The nile cruise is the way to go for southern Egypt (Luxor and Aswan). Most river cruises have meals that are not buffets, but you can inquire before you book. We had great food on ours.
I am serious, I lived in the Middle East for five years and had Egyptian friends. Egypt is not like going to Europe at all.
On the other hand, if you go and see the wonderful sites, it is amazing.