I've been to Luxor twice (airline) and Cairo and to be honest there is nothing to see in Egypt from the air - outside of a very few spots.
The pyramids are in Cairo, not outside in the desert. But I know of people who were allowed to fly an orbit around them while transiting, so some unofficial things are possible - like refuelling at "6th October". But once you have seen the pyramids you have seen the pyramids... the main advantage of doing it from the air (IMHO) is that you don't get ripped off some euros for using a toilet.
Luxor is much better but to see e.g. Karnak Palace you would need to be very low. I think I saw somebody doing pleasure flights, but it may have been something else "piston".
The rest of Egypt is totally barren - hundreds of miles of absolutely nothing, zilch, zero. Many hours flying. Better bring some serious survival gear, with food etc.
Getting permissions is possible only via overflight agents who "arrange" stuff like visas and overflight permissions by "lubricating" "contacts" in their government. That's how Egypt runs.