Private repositories are great for closed source projects. Private repositories help you save your code without having it in the open. Such as programs that are proprietary for you at the moment and that you don't want to share. Any software developers who want to try something new, experiment with a new language or start a project they don't want others to know about will not have the associated source code be part of the public domain. That's awesome.
For organization-owned repositories, private repositories are accessible to the repository owner and the people the owner share with. Still, the repository can be forked by the collaborator and the collaborator can add third-party collaborators. Isn't it somehow weakening the power of the private repository?
Least importantly, the popularity of GitHub was growing with the ability to find code written by fellow developers who previously solved your problem is one of GitHub's biggest contributions to the programming community till now. With the option to make the public repository private and private repository for the free account, let's hope the option to create private repositories won't truncate the number of code developers share openly and publicly with each other.