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From the article:
But for the general public, the implications of the study are simpler. “A microwave is not a pure, pristine place,” Porcar says. It’s also not a pathogenic reservoir to be feared, he says. But he does recommend cleaning your kitchen microwave often — just as often as you would scrub your kitchen surfaces to eliminate potential bacteria.
it’s like any other surface anywhere - even if you clean it regularly it will still have bacteria on it. but the thing is most bacteria are not harmful.