I wouldn't read that much into it; WhatsApp is simply more popular so they would face too much of a backlash. That would be my guess.
So, for me the question remains: If what the Egyptian government wants is to apply their surveillance policies and Signal is banned because it is preventing them, doesn't the continuation of operation of other "private and encrypted" messangers say something? Especially of Whatsapp that claims that it implements the same security and privacy oriented architecture as Signal does?
[1] https://www.freedomhouse.org/report/freedom-world/2013/egypt
No man rules alone. Even in a dictatorship, pissed off peasants mean an army that has to do horrible things to keep them in line. That costs a dictator money.
In most cases of dictatorships, people end up being kind of pissed off against the dictators. That's what it takes usually for people to call their rulers "dictators". It is not how you would call someone you like. Exactly for the same reason, the more authoritarian the establishment is - the less they respect/support liberties, personal/political rights and privacy of the people: Because the establishment expects such rights and liberties will be probably used by the people against the establishment itself. And exactly this is why such liberties and rights MUST be protected always, by all costs.
I am not Egyptian myself, but through discussions with Egyptian friends and/or Egyptians I randomly met, this is what they think of their government.
This is getting off topic so I stop it here.