Why do you think most of Egypt was mainly desert?

It depends on how the question is read:

Why do people say that Egypt is mostly desert? -- Because it is. Most of Egypt gets minimal rainfall and has long patches of arid land. That is the definition of a desert. Over two-thirds of the country is made up of the Sahara Desert.

Why is Egypt a desert? -- The moisture bearing winds that blow from the south and the west lose their water over the Atlas Mountains and the West African coast respectively, making the Sahara incredibly dry.