Github is a hosting service built around git. Likewise, gmail is a service built around e-mail protocols. It's fine for services like these to exist because you

Github is a hosting service built around git. Likewise, gmail is a service built around e-mail protocols. It's fine for services like these to exist because you have a choice of whether you want to use them or not to facilitate the use of the underlying protocol (you are free to set up your own e-mail server if you want, and doing so does not prevent you from communicating with users who choose to use gmail). I think rather the big issue is, for instance, the use of Facebook Messenger for IM. If everyone I know uses it, I have no choice but to use it too because there is no underlying protocol behind it.