I am all for giving hate to flash. It is commonly found vulnerable. It produce slow websites which eats memory and cpu. It has poor history in non-windows systems.
But in all, I have serious doubt this call was made for any reason beyond pushing users to their app-store. games? online experience? chat? By forbidding flash, companies are bit more forced to turn to apps with their products. Sure, things can still use javascript, html5 and web-sockets, but I would not trust web-sockets to be left alone if they seriously would start to threaten the app world.
Maybe I am just cynical, but follow the money argument looks to support it.