I feel like I'm missing the joke. The section "hating on" Times New Roman is displayed in the font-family Times New Roman. Is the author just having some fun?

Yes, I think he's just being clever. If you look at the source you can see the font choice is explicitly set inline, for this page only:

    <div style="font-family:Times New Roman;font-size:105%">
      ...
    </div>

So, it's definitely intentional. Moreover, because the rest of the book is typeset in Equity, a Times New Roman replacement the author designed, we have the opportunity to see and feel the difference. It's a kind of "show, don't tell" statement. I think it'd underscore the point better if the last paragraph pointed out that everything you just read was typeset in Times New Roman and then link to a page with the same article typeset in Equity.

I went to another page of his and copied a paragraph, setting one paragraph to use Times New Roman and another to use Equity. Without saying which is which, I'll leave it to you to decide which is "better": http://cl.ly/image/0I333L3d0O2H

I suggest not "cheating" by comparing the font shapes to the example Equity at the top of the page. :D

Trying to make a point, perhaps?

Did you read that? I seriously doubt your reading comprehension skills if you characterize what he wrote as "hating all over Times New Roman".

> Times New Roman is not a font choice so much as the ab­sence of a font choice, like the black­ness of deep space is not a col­or. To look at Times New Roman is to gaze into the void.

For an example of a good (or at least unique) usage of Times New Roman on web design, take a look here: http://seedconference.com/seed.php