The probiotic bacteria that are supposed to inhabit our gut evolved right alongside us over millions of years. They evolved to inhabit our gut and resist whatever Antibiotic properties our food might have.
Iodine is a nutrient required for the human to stay alive. Hence, Iodine should not kill off the probiotic bacteria in the gut because that bacteria evolved to resist the Antibiotic effects of Iodine (and the other nutrients we ingest).
The "bad" bacteria, however, did not evolve in this way because they are not supposed to inhabit our gut.
Any bacteria that die due to the ingestion of a nutrient never evolved to resist that nurtient. Any bacteria that do not die off did evolve to resist that nutrient.
It's pure speculation, but the Iodine should kill what isn't resistant (what doesn't belong) and should not kill what is resistant (what does belong).