The accepted answer works, but you have to do a "Select All" first -- every time -- and I'm way too lazy for that.
And it turns out, it's not super trivial -- I figured I'd post this here in an attempt to save like-minded individuals the 30 minutes it takes to track all this down. -- Also note: this approach restores the original selection when it's done (and it happens so fast, you don't even notice the selection was ever changed).
1.) First, add a custom command to your init script (File->Open Your Init Script, then paste this at the bottom):
atom.commands.add 'atom-text-editor', 'custom:reformat', ->
editor = atom.workspace.getActiveTextEditor();
oldRanges = editor.getSelectedBufferRanges();
editor.selectAll();
atom.commands.dispatch(atom.views.getView(editor), 'editor:auto-indent')
editor.setSelectedBufferRanges(oldRanges);
2.) Bind "custom:reformat" to a key (File->Open Your Keymap, then paste this at the bottom):
'atom-text-editor':
'ctrl-alt-d': 'custom:reformat'
3.) Restart Atom (the init.coffee script only runs when atom is first launched).