None of us know what comes out of your tap, so none of us can answer that. Personally I drink untreated well water, and occasionally untreated stream water. Lots of bacteria, mostly E. Coli, in my stream water, quite a bit less in the well water that flows from my tap. I know this because had it analyzed before I bought the property. I recommend you analyze your water source, too.
They are quite literally everywhere. There are some in the room with you right now. Don't look!
Personally, I am living in harmony with them. I don't know what you are doing.
I thought the article covered that pretty well. If you don't over-sterilize your environment, and keep a healthy heterogenous bacterial environment around you, on you, and in you, then they pose no significant risk. If you habitually and obsessively use hand sanitizers, broad-spectrum antibiotic medicines, or bactericidal cleansers and wipes, your risk goes up significantly, because those things destroy all micro-organisms without destroying the food sources micro-organisms live on - in fact, when you sterilize water you increase the available food for micro-organisms. Then the first thing that lands in the sterile area after the poison wears off will "bloom" - remember, most micro-organisms reproduce asexually - and this can create a potentially dangerous large bacterial monoculture. Your body can easily deal with two or three dangerous soil or water microbes at a time, it's doing that right now - but your immune system cannot so easily deal with billions of them.
If you own property, here's an easy way to strengthen your immune system: practice chemical-free gardening. When you weed the dandelions and chickweed out of your yard by hand, you will expose yourself to prophylactic doses of the very germs discussed in Maggie's excellent article, and strengthen your immune system. Oh, and don't use "hand sanitizers" of any sort, sneeze in your elbow, and consume plenty of fermented or brewed foodstuffs, and do something nice for your mother next Sunday. There, now you're covered.