There are a whole bunch of "networks" of fake accounts, often complete with very legitimate looking photos, names, and even posts. The main difference, however, is they follow and retweet a lot.
If you look at what they follow and retweet, however, well over half seems to be "legit" stuff that wouldn't be getting involved in such schemes. I think the reason is that if Twitter decides to crack down on bot networks, they might look at what the bots are following and promoting to work out who to penalize.. except they aren't going to start deleting CNN, Fox News or random celebrities.. so they really have no great way to tell who to punish. I suspect FB bots work in a similar way.
The article suggests USA Today brought this to Facebook's attention. If USA Today had been doing this on purpose, even indirectly, that would be a bizarre move. We also have nothing from Facebook contradicting this claim.
You can hypothesize nobody asked Facebook about it or that USA Today is now lying to try to save face, but those would be hypotheses that are possible, but not currently supported by the facts. It is a reasonable interpretation that USA Today is indeed a target of some sort and not the instigator. I am also not sure exactly what the bots sought to gain from this, but I've seen enough similarly crazy things that made sense once an explanation came out that I'm willing to give some time for such an explanation to come out.
I've got no love lost for the media but they're still shining beacons of virtue compared to the people authoring and running bot networks for this sort of thing, so I don't find it that hard to trust USA Today enough to consider their version to be the most likely story. (Not the only story, but pending further data, the most likely one.)
1. They didn't break the story, CJR did.
2. Why would they buy so many likes? In my experience, native ad sales revolve around native metrics. Buying bots to like your page (but not visit or interact with your website) won't help you there.