Add to this that those using a combination antibiotic protocol (CAP), at least on the CPn Help website, describe a big reduction in recurrent infections while on the protocol, and the use of high dose zithromycin reducing asthma and the like which you can read on http://www.asthmastory.com/
and I would not worry about this too much.
In the Chlamydia pnemoniae research you see study after study linking, for example, Cpn to heart disease. Then you see studies which are taken as the final arbiter's of the issue which used a single antibiotic (monotherapy) to treat or prevent heart disease with no significant result. From this it is concluded that treating Cpn is not effective for heart disease, let's look elsewhere (you find the same thing in MS). But... the studies clearly don't understand the persistence of the organism in multiple phases, and not one of them uses a CAP in determining prevention or treatment effect.
The same with this simple and highly simplistic study of tetracycline use and infection rates. Makes for a nice, quick and dirty publication to aid someone's academic career, but doesn't ask any really meaningful questions, and like many clinical studies, is done in ignorance of the bacteriology involved.