Being an Egyptian myself, I have some information about this subject.
But my information is also supported by an Egyptian Egyptologist called "Ossama Al-Sa'dawy" who has a PHD in the Ancient Egyptian language.
My sources are his research papers and his dictionary, and he states (And again, me being an Egyptian I can confirm) that a lot of words that modern Egyptians use come from the Ancient Egyptian language.
We actually use these words on a daily basis and most of us Egyptians do not even know that these words come from Ancient Egypt, but what everyone knows for sure is that these words are not Arabic in anyway.
In Modern Egyptian language, if the word's origin is not Arabic, then it can be English, French, Italian, Latin, Turkish, Spanish and of course Ancient Egyptian.
I cannot say how much exactly of the language now comes from Ancient Egyptian, but from my own experience and being born and living in Egypt for 28 years (And using Dr. Ossama's research), I can say that there are no more than 50 words that today's Egyptians (actively) use that come from Ancient Egyptian directly. Including names of areas, cities, towns and villages.
-We use the word "Nannus" as a cute way to refer to a baby, Ancient Egyptians used that word to say "The beautiful one"
-We use the word "tata" to encourage a child to take his first step, Ancient Egyptians used the word "titi" that means "Pace" or "tread"
-We use the word "Embu" to refer to drinking water, and Ancient Egyptians used the word "embe-mo" which means "from the water"
-We use the word "Bahh" to say "finish" or "end", and Ancient Egyptians used the word "phh" which means the same "to come to an end"
-We use the word "haba-haba" which means "easily easily" or "bit by bit" and Ancient Egyptians used "hbhb" which means "tread" or "trample"
Unfortunately most of his work is in Arabic, but you may find some interesting information in his messages and his dictionary.
You will find some great information about this very subject written by him here as well.
A great book written by the American University in Cairo in a story format that uses a lot of Ancient Egyptian words that are still in use today in Egypt:
"From Pharaoh’s Lips:Ancient Egyption Language in The Arabic of Today - Ahmad Abdl-Hamid Youssef"