Tapeworms have a parasitic relationship whereas most gut flora usually has a symbiotic relationship with the host.

The line is kind of blurry, and it get's complicated, but there is no such thing as a sterile gut under normal condition. Hosts and "guests" have evolved together, so most gut bacteria won't become a problem most of the time. Exceptions abound, of course.

Tapeworms on the other hand have tons of side effects which the original donors of the gut bacteria don't seem to display...