The default setting in Atom 1.x seems to be to not show the invisible characters. I tried to search how to enable this but I only found answers for old version . I had to go to the documentation page which was not easy to find so I am posting the solution here.
To enable showing invisible characters, all you have to do is open config.cson file (Atom->Open Your Config on Mac OS X) and add showInvisibles: true under editor so that the config file looks like the following:
editor:
invisibles: {}
showInvisibles: true
Hope this helps!