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I think patients hear mixed opinions about this question because nobody wants to tell you to ban all of your pets from the house, even if they present a risk. Most pets spend some time outdoors where they can collect bacteria, some pets may harbor parasites like fleas and ticks, and pets can't be kept sterile. Avoiding the litter box is an obvious precaution. Beyond that we hope it's only a small risk, but it's probably hard to judge.
Why don't all patients play it super-safe and keep all pets away for some number of months post-transplant? They could, but for many families this presents practical problems. Pet boarding is expensive. Friends and relatives may not want to babysit a pet that long. Even more importantly, pets are members of the family. You care about them and their feelings, value their loyalty and affection, enjoy giving them attention, relax by petting them and playing with them. Risk or no risk, they are part of your life, help you feel normal, and are part of your support system.
The way I think of it, it's not really a medical question as much as a personal decision about the value of your pet's companionship, the disadvantages of having them live elsewhere temporarily, and the level of risk you feel comfortable with.
When my wife had her bone marrow transplant we were lucky to have some wonderful neighbors who were more than happy to keep our dog for 100 days (my wife's "home quarantine" period), so we got to play it safe, with no pet in the house. Our kids could visit our dog a few blocks away and our dogsitters took our dog along when they went on hikes so we knew he was getting great exercise and fun. Yes, it felt mean not to let him stay home, but dogs are very forgiving and once he was home again it was just like old times.
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