For New Projects
To create a private project go to the Add Project page, and select the Private checkbox. The created project will only be readable to project members, and its contents will not show up in search results.
For existing Projects
If you have an existing project that you wish to make public, you need to change the project permissions at the Admin panel (Admin -> User Permissions) and remove all permission from the Anonymous and Authenticated groups.
Remember that if you have previously customised your project, or if you have sub-projects you will need to check the permissions for those as well.