Atom – disable single key binding

1. Open settings with File > Settings

2. Click Keybindings

3. Filter the list by typing ctrl-alt-= in the search box.

4. Click the clipboard icon next to the shortcut. This will copy the shortcut definition to your clipboard.

5. Click the hyperlinked text your keymap file.

6. Paste in the contents of the clipboard.

7. Replace 'pane:increase-size' with the value 'unset!'

Now ctrl-alt-= will not do anything.

EDIT: 'unset!' was previously null, see this atom discussion for details.

EDIT2: To fix issues with many non-QWERTY keyboard layouts, check out the keyboard-localization package for Atom.