Yes, using nmap, metasploit and meterpreter totally makes you a hacker.
Seriously 'security' and 'Microsoft' do not play well in the same sentence.
You're just being unnecessarily deflationist and reductionist. You're missing the article for its words (missing the forest for its trees).
This notion of being a hacker due to using a tool is preposterous. The only thing the article does is perpetuate the flawed understanding of computer security and hacking for the general public.
Like, you're just not reading the article. You're just not. The fact that the OP mentions "getting physical" is an obvious counterexample to your criticism and reduction of "it's a list of "hacking tools"'. Can you see the narrative (the forest)?
No one calls Linux "a tool" in the sense you're talking about. The OP is saying, with that subheading, "If you're just some Windows [power?] user, you've got to radically change that" — or even further, "If you don't know that OS X is *nix, to say the least, you've got to radically change that".
I mean, it's The Guardian for Chrissake. What do you expect, a list of dotfiles with rich comments?