I highly recommend La Nacional in Roma, where you can enjoy some bottled brews by Cucapá, as well as a large variety of other nationally made drinks like Mexican vodka (?). Zazá is also a great place. They only serve draft beers, primarily Tempus, Calavera, Cosaco and Azteca. However, since they only have beers on tap, and taps run out all the time here, it is really anyone's guess what they'll have available on any given day. They also make amazing pizzas at Zazá, so go hungry.
One comment on the article. At the beginning they state: "These national drinks are considered some of the best in the world for their aroma and variety." While Mexican microbrews need all the help they can get, this is a little over the top. Some of them are very good, some of them are very very bad. This industry is still in its infancy and they are bound to make a few missteps. Nevertheless, most of them are at least better than the beers produced by Modelo or Cuauhtémoc.
I'll reprint the list here (with the correct address for La Nacional, Publimetro got it wrong). I've divided up the places by colonia with the name of the place first, followed by the street address. I'm excited to check out the place in the Centro Histórico, since (in my somewhat limited experience) it is generally a wasteland for good food and drink.
Pujol, Petrarca 254
Jaso, Newton 88
Boca 21 Deli, Amsterdam 36-A
La Nacional, Querétaro esq. Orizaba
El Deposito, Av. Baja California 375
Makena, Tamaulipas 56.
Zazá, Pachuca 1 esq. Veracruz.
Miralto, Madero 1, Piso 41 Torre Latinoamericana.
Barraca Valenciana, Monterrey 220.
Centenario 107, Centenario 107.