You misunderstand what the tree view is. Atom is designed with the idea that each window is a “project”. The tree view displays the set of folders you have open for that project. You can easily add additional folders to your project with the Add Project Folder menu item (it’s both in the context menu and under File). You can use a project management package to store these multiple paths and reopen them (in order to get back to the editor state you had last time). If you want to open a single file without adding another project folder, the standard File -> Open File menu item works fine.
This FAQ entry has more information on the way Atom thinks about projects and its logic when starting up:
If I might add a small piece of advice to what @DamnedScholar just said, a quick solution for the file opening issue only is the advanced-open-file package, that allows you to quickly open any file on your system without take your hands off the keyboard. It is actually quite handy.