Welcome to the forum.
Initial response to the title you came up with, before I read the question itself: For almost all STDs and genital health problems, the test results are far more reliable than symptoms. If you have been tested for herpes, syphilis, HIV, or whatever -- pretty much no matter what you say about symptoms, the negative tests are reliable and the symptoms are not. You do not have whatever STD you tested negative for.
Now I have read the qeustion itself. You can be sure you do not have gonorrhea or chlamydia. The only other STD that could explain your symptoms is NGU, but that also is unlikely. First, NGU usually causes discharge from the penis, not the urinary urge you describe; and second, NGU would have cleared up on doxycycline.
Like a very large number of questioners on this forum, I suspect you have a prostate gland problem or the chronic pelvic pain syndrome. Most such problems are not due to infection of any kind; the cause of most prostatitis is unknown. Neither prostatitis nor CPPS are STDs. Another common explantion for such symptoms is genitally focused anxiety, which is very common when someone has a sexual indiscretion they regret. Indeed, CPPS and genitally focused anxiety are often related.
In other words, I agree with the doctor or clinic who told you "not to be concerned and that it could be prostatitis". I believe you have nothing that will ever be harmful to either you or your regular sex partner, and if I were in your situation, I would continue unprotected sex with my wife without fear. For more information, I suggest you do some online searching; you could start with google searches for CPPS (spell it out) and/or chronic prostatitis. The Wikipedia article on CPPS is quite good. Take a look; I'll be you see a lot of parallels with your own symptoms.
I hope this helps. Best wishes-- HHH, MD
Thank you Dr, your input is appreciated.
Just so I cover all the bases...
I will do further testing for all STD's to alleviate my concerns but the symptoms would not suggest it was a different STD aside for the ones I was tested for correct?
Finally, I did have sex with my regular partner prior to the symptoms and thus prior to the antibiotic treatment. You say the risks of it being an NGU are low, I assume I should not be concerned about unintentionally passing anything on to my regular partner before I was put on Doxycicline?
No other STDs could cause the symptoms you describe and no other STD tests are necessary. Since you almost certainly had no STD, I doubt there was any risk to your partner from the sexual exposure before you started treatment.