The olfactory epithelium allows external substances deeper into the body tissue than other boundaries in order to enable the sense of smell.

You can inhale (or be exposed by a wound in the skin) a single droplet of water containing Acanthamoeba and get sick and die. That would be a rare occurrence, but it does happen.

You can drink 10,000 liters of water full of it and never get sick, it rides down the slip-and-slide of your throat into your stomach where your stomach acid destroys it. It is likely that half of all people in the United States drank some today.

Several types of bacteria are like this, like staph and legionella, you can eat and drink them but the second they get in your nose or lungs (or blood via a cut or scrape): no bueno.

Unless, like the article suggests, you have an immune-compromising condition you have very little to be afraid of.

Just don't go swimming in warm stagnant water no matter how healthy you are.