There are lots of types of perfluoroalkyl compounds in existence, and they very greatly in their properties. The first thing to note about PFASs is that they are the salts of saturated carbon-chain sulfonic acids, like most detergents, and their primary use is as surfactants and emulsifying agents (longer-chain PFASs would also function as detergents, but it is the medium-length PFASs that have found most use in industry). The anionic (salt) nature of these compounds is presumably responsible for their ability to associate with enzymes and other proteins, possibly disrupting their normal function.
Perfluorocarboxylic acids (which, like PFASs exist as anions at biological pHs) behave in a similar way, and have similar industrial applications. Pefluorooctanoic acid (PFOA) has been most studied in this regard; Among PFASs, perfluorooctanesulfonic acid (PFOS) has likewise seen the most application and been most studied as a pollutant.
Unfortunately, there are other PF compounds that can degrade to form PFCAs on oxidation. Basically, the PF portion of the molecule is extremely inert to chemical attack, but any side chain which is not perfluorinated can be oxidized to yield, ultimately, PFCAs. PF chains which include C=C double bonds (i.e. unsaturation) can be similarly oxidized. The result is that there are lots of sources of PFCAs other than the actual manufacture of PFCAs. Many products that incorporate PF side chains are formed by a process known as telomerization of tetrafluoroethylene (TFE) and are prone to formation of PFCAs both in the mfging process and on degradation.
Unfunctionalized perfluorocarbons, in contrast, are quite harmless and have been studied as artificial blood substitutes. And Teflon, basically a long-chain perfluorocarbon, has been used safely in surgical implants for years (problems associated with PF coatings arise from PFCAs used in the manufacturing processes as emulsifiers).
It's hard not to notice a certain irony here: The thing that makes PFCs so attractive as structural materials and coatings is their extremely low chemical reactivity. But to use them as surfactants -- that is, materials which alter the surface behavior of other materials (such as stain resistance, see ScotchGard) -- it is necessary to add a little reactivity to part of the molecule in order to form a bond between the PF material and the non-PF surface. But once the non-PF functional group is introduced, that becomes the Achilles' heel by which the PF coating may be degraded to a PFCA and be lost to the environment, thus becoming a pollutant. So while a completely saturated PFC is safe, changing even one atom to a non-PF center makes it unsafe in the long term.
{ETA: But PFCs, sold as bulk commodities, have low profit margin. Specialized applications such as surfactants can produce large, desirable practical effects from application of a small amount of material, so profit margins can be pushed a lot higher. Just in case you're wondering "why did anyone ever make this stuff ?", it's the invisible bloody hand of the sacred Free Market at work again, in all its subtle ways.}
CFCs -- chlorofluorocarbons -- are also notably unreactive, which is how they manage to survive long enough to diffuse into the upper atmosphere where they are degraded by UV light to form ozone-killing chlorine atoms. But like PFCs, they are essentially harmless biologically, though they do function as anesthetics (by means not fully understood).
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