Elaine Gotschall was differentiating positive and negative species 20 years ago. Some species that people take for granted as being beneficial are not necessarily beneficial.
If lineup is correct that protozoa feed on bacteria, and I have no reason to doubt this, then they are just another part of the natural ecosystem. parasites feed on gross physical waste, bacteria feed on smaller particles, and protozoa feed on yet smaller particles/bacteria. This makes me think that protozoa are the least of the real problem and people are once again mistaking the tip of the iceberg for what looms underneath.