Why are these compounds hazardous?
- Harmful biological effects in the human body, like hormone-mimic activity.
- Low molecular polarity leads to bio-magnification in fats and oils up through the food chain, and persistence in human fat.
- The high strength of the carbon-fluorine bonds greatly reduces the rate at which typical environmental degradation mechanisms (hydrolysis, photolysis, atmospheric oxidation, enzymatic breakdown in cells...) act on these compounds, compared to their hydrocarbon counterparts.
Why are these compounds used?
The same properties that make them hazards once dispersed -- strong carbon-fluorine bonds that resist breakdown, low polarity -- make them desirable in applications where people want water-repellant surfaces or materials that resist high temperatures and/or chemical attack.
Why weren't the risks better known before?
It's a lot easier to test for acute hazards than for chronic ones. By acute toxicity metrics, like feeding a bunch of rats these compounds until the dose is high enough to kill half, these materials are generally less toxic than substances like potassium fluoride. It turns out that for low level chronic exposure, perfluorinated compounds are more hazardous than simple ionic fluorides due to persistence and accumulation.
The link between stability and persistence makes up a recurring theme in environmental toxicology: materials with lower acute hazards are often worse hazards in the long term. The very lack of reactivity that makes molecules less acutely hazardous in case of e.g. a fire or a worker accidentally splashing some on skin makes them more likely to be long term problems, because the same basic properties impair how quickly environmental sinks can break them down. Pure methanol ignites more easily than diesel fuel and has worse acute toxicity risks if a worker gets drenched in a spill. But diesel contamination from a leaking storage tank is more persistent.