The issue is there's a lot of interesting science which looks suspiciously like it's being monetized into some handwavy - and potentially dangerous - claims.
For example the idea of bacteria protecting you is not so simple. They don't target "bad organisms" - there really aren't bad organisms. Monocultures are bad because they have no competitors. A mixed-ecology where you have several or many species which do compete usually inhibits the ability of any 1 type to take over successfully.
Of course, this is all happening on the surface of your skin, and how stable is that environment anyway? History says not very - and on top of that pretty much all of these things are really nasty if they successfully get under the skin.
One successful way to treat IBS-like symptoms for example is to take a course of antibiotics which are known to be mild - that is, they tend to have a balancing effect on the gut's fauna. I can personally attest this makes all the difference in the world.
Conversely, it's not at all clear that probiotics do anything - for reasons similar to the above. In a crowded environment, they can't easily take over, and bacteria are all about film-forming and quorum sensing and the like - isolated cells are much less active.
On top of those issues, there's a scale one. Humans basically regard about 150-500 people as being actual human beings like them (Dunbar's number). Historically we tribalized on that sort of scale but almost every culture started to use various scents or cleansing practices when they built larger and larger groupings. Sure, maybe we can get by with intact surface cultures, but can we get along? The human nose is important. Try being in a room with someone who has a bad smelling odour - the urge to simply leave is powerful. The urge to try and wash it off is powerful. Its not clear that we'd be at all tolerant of people who smelt sufficiently different - and I suspect that's why we standardized on a zero which we can all achieve.