Went to Egypt with my partner last year. No problems at all. We didn't do anything particularly gay oriented so did not feel threatened at all. Egyptians are very friendly. Beware of organized tours!! Better to scope things out yourself.
Though men are generally affectionate towards each other in Egypt, don't mistake that as homosexuality. It is simply friendship.
We stayed at the Sofitel Le Sphinx in Giza. Wake up to the view of the pyramids of Giza - just simply breathtaking! No problems getting one king size bed and no strange looks as well.
I would recommend paying for paper tickets. E-tickets are a new concept there and could pose some minor hassles. Check in desks were PAST security which meant you need to show your tickets to get pass security. E-ticket holders are listed on a paper list but often the security guards are clueless. If flying out of Cairo on an overnight flight, prepare for a madhouse at the airport as almost all the flights to Europe depart then.
You'll have an experience of a lifetime!