To jump from "This might be a cause" to "Lets treat people with long term courses of antibiotics, which have known and often severe side effects" is a pretty serious leap in logic.

And I know very few clinicians who would tell someone who believes they're suffering from "Chronic Lyme" that they're not sick. Just that they're not sick in this particular way. Non-specific, widespread inflammatory disease is something the medical community is still struggling to figure out. But antibiotics are fairly nasty drugs for "We have no way of diagnosing this, fleeting evidence for a causal link, and no population-level studies."