The branch doesn’t exist yet; you need to commit something first.
Edit: I’m not sure what you mean by “master repository”, but I’m referring to the branch called
master which is commonly used as the main branch.
Initialize a Git Repository button doesn’t do anything except run
git init in your project folder. You still need to perform the normal tasks for setting up a repository from the command line, including setting remotes, but you can make the initial commit inside Atom using the Git tab that you see in your screenshot. You can skip those steps by cloning an existing repo, in which case Atom’s git integration will “just work” with no extra effort on your part.