You must not have watched the Ted talk which makes a very compelling case to why its a bad flag. The video talks about how great flags, like chicago's, are flown everywhere and bad flags are not.
I grew up about an hour north of Chicago and an hour south of Milwaukee; I visited and worked in both cities. I've never seen the Milwaukee flag but I always saw the Chicago flag around.
I think you're the one missing something; namely that while the TED talk cites Milwaukee as a bad flag, the author (Whet Moser) of the linked article (which embeds the video) describes his disagreement. Hence the "too" in "I like the Milwaukee flag too" means "as Moser does", not "in addition to (other flag)".
Whet doesn't hate the Milwaukee flag as much as Roman Mars, but he agrees with that the Chicago flag is superior. (The TED talk doesn't cover this, but Whet's actual article does.)
I grew up about an hour north of Chicago and an hour south of Milwaukee; I visited and worked in both cities. I've never seen the Milwaukee flag but I always saw the Chicago flag around.