Both are hosts to the fleas that spread bubonic plague. There's a reason people have been trying to eradicate them for the last century.
The situation is a bit more complicated and nuanced than that.
At an American Society of Microbiology conference a few years ago, I saw a presentation on the problem of plague in prairie dogs. The scientists of the Fish and Wildlife service wanted to eradicate the plague. So they hatched a plan to fumigate the prairie dog burrows to kill the plague-carrying fleas. The farmers and ranchers wanted nothing of the sort to happen. They wanted the plagued fleas to remain because the plague is very deadly to prairie dogs and can wipe out whole populations of the dogs. What happens is that a colony of prairie dogs builds its warren of tunnels, which can become quite extensive, and if a dog encounters a diseased flea, the plague quickly spreads and kills the entire colony. The empty warren is then full of hungry fleas, and stays empty for years until the fleas and bacteria die off. Thus, the farmers and ranchers depended on Yersinia pestis to control the dogs, which they did not want on their property.
The ferrets, IIRC, almost died out because they got distemper from dogs. Protecting their population (by vaccinating with the food-baits) will let them breed, and they will once again control the prairie dog population.
It seems to me that the farmers might become more amenable to other plans to wipe out the diseased fleas, if there is another (natural) method to control the rodents.