Atom (and most other "tabbed" applications) isn't limited to just tabs-- it supports both multiple windows and arbitrary splitting inside a window. Tabs can be dragged and dropped freely between any pane. So, you can have tabs when it works well (IME, for the type of text editing one is doing while writing code, you're usually only actively using one file at a time, much like in a web browser), and you can have more than one file visible when you need that too.

(File management, on the other hand, is completely different; there, you're almost always going to want to have more than one thing visible and a windowed interface is better. That's why no mainstream file manager supports tabs OOTB.)