It's probably the fact that shower heads have so much more surface area for stuff to grow on and live in. One minute it's wet, and then it's drying for the rest of the day. A water faucet is less hospitable to growing gunk.
Hmm; I could see it being the exact opposite. The shower head, by drying out after a single daily use, could be less hospitable to organisms that need moisture. Meanwhile a faucet, used several times throughout the day, has areas which never dry completely.
They're studying human microbiome, not the health impact of drinking different stuff. Anything living in your showerhead is going to get deposited on your skin every day, so it may be a reservoir for your personal microbes, or something that interferes with them.
there's an element of aerosolisation with showerheads, so you might be breathing this stuff in.