But why would anyone use Whatsapp after the Onavo stuff?
Was it forced into Whatsapp somehow?
IMO the answer to your original question is: lock-in effect. People are generally too lazy to move to an alternative, and on top of that, if they decide moving to one, they don't necessarily know which one to chose. And many privacy-advocates don't help by being (again IMO) too extreme: "Do NOT use Signal, you MUST use <choose your complicated ultra-secure alternative here>".