Person who worked for years in arthropod borne disease control here.
Except for the reporting screw-up about virus vs. bacteria, this is all just quibbling. The reporters got it wrong as usual, but that doesn't mean that the researchers got it wrong.
Zoonotic diseases (ones that spills over from one animal population to another) always have fantastically complex life cycles. In epidemics of zoonotic diseases it's common for epizootic transmission (transmission between species) to be overtaken by enzootic transmission (transmission *within* a species). For example influenza is a bird pathogen that can cross over into mammalian species like swine and humans. If flu epidemics didn't shift gears from epizootic transmission (bird to human) to enzootic (human to human), they wouldn't be as big a deal. Just stay away from chickens.
So the idea that the black plague was primarily spread among humans enzootically is hardy groundbreaking epidemiology. It certainly doesn't mean that it's not dangerous to live in a place infested with plague-ridden rats. But the shift to enzootic transmission is something that's a bit different from the mosquito or tick borne diseases or occasional, isolated epizootic plague infections we're largely familiar with today.
It's a neat finding, in that it wasn't necessarily expected, but it makes sense in retrospect. In something like West Nile Virus, the natural focus of the pathogen is migratory bird populations that fly thousands of miles. But while a rat can hop on a ship and travel thousands of miles, the vast majority of rats spend their entire lives in a radius of a few hundred feet. Humans are much more mobile than rats; even if a few rats hitch a ride on a ship, they never go anywhere far *without* humans.
What's simplistic is the assumption there has to be only *one* factor involved in a zoonotic epidemic. Without epizootic transmission the plague would not have happened in the first place. That's not news. Without human-to-human enzootic transmission it would not have spread so widely or kill such a high percentage of the population. That is news (I guess -- I didn't work with people doing plauge so I have no direct knowledge of what people in that field thought). Of course before it becomes established science it's going to have to stand up to criticism for a few years.