Typing a TAB in atom.io results in a TAB on the screen. It behaves like a TAB while typing and it's still a TAB when re-opening that file.
However: while stored to a file, it is actually not a TAB anymore...
Check yourself using "cat -e -t -v" ... TABs are (...should be...) indicated as "^I".
I know there's some pretty radical SPACE-racists around, but... come on guys!!! Isn't that a bit _too much_ for an _plain-text_ editor? You'll never be able to save a Makefile with this magic going!!!
There's a bug open for already two month, now... https://github.com/atom/language-make/issues/3