I had the same problem, in the end used SwissAir, you can book online to Cairo via Zurich (about 1 hour stay) then internal flight via EgyptAir (also booked online) they have few flights a each day so not too much waiting around.
It's not the most direct or fastest way to get to Hurghada, but at least you have more flexibility then the charter airlines, the 1st time I went there with XL air, I had a 9 hour delay at Gatwick which nearly put me off Egypt all together.
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