Persistent urethritis is an inconvenient conundrum for patients and health care providers alike. But the important thing is that it is not at all serious, i.e. has no known long-term health consequences for either you or your current or future sex partners. Repeated antibiotics probably won't help. The best guess is that the initial inflammation caused by chlamydia (or other causes of NGU) starts a vicious cycle of inflammation that is due to an aberrant immune response, not to continuing infection.
As to the rectal problem, I'm not sure it's the same problem. It sounds like you have proctitis, the medical term for inflammation of the lining of the rectum. I doubt an infectious agent is causing either that problem or the urethritis, and I doubt something was actually transmitted from your urethra to your rectum.
Herpes is a remote possibility for the proctitis, and even more remotely for the urethritis. Consider a blood test for HSV-2 infection. (See many previous messages on this board about the proper kind of herpes blood test.)
If a gastroenterologist isn't involved in your care, that might be a good next step to assess the rectal problem. I suggest you stop worrying about your mild urethral symptoms, which probably will eventually fade away. And stop taking antibiotics. One (remote) possibility is that either or both problems might be related to the effects of long-term antibiotic therapy.
Good luck-- HHH, MD
Thanks