Cool. Sometimes you just have to be amazed at evolution. The fact that we could have evolved a set of, what amount to pattern recognition receptors specific to microbial proteins sort of makes me feel like a tourist gawking at the tall buildings.
OT, but interesting is the role TLR’s might play in some autoimmune disorders.
But it has everything to do with the Hygiene/Old Friends Hypothesis mentioned upthread: The “right dirt” activates various portions of this system to various degrees which allows it to exert the complex regulatory functions that article scratches the surface of. Without enough exposure to the “right dirt” (perhaps even as part of our resident microbiota) these receptors are not as well regulated and can get triggered by portions of self. Without adequate regulation these substances are not completely selective for non-self vs self.
It also has to do with the potential confounding difficulties of exploiting these systems – inadvertently triggering autoimmune and/or allergic responses.