Penis Pain/Itching. Is it an STD, Infection?

I am a male and always seem to have painful ********* following protected *** (with my gf) and for the following day. I also have had itching inside the ***** head for around 4 months which I believe occurred after an incident where the condom broke and I was exposed for around 25 seconds. I went to the doctor and have tested negative for gonorhea, chlamydia, hiv, and herpes. The doctor said the itch could be herpes but I dont have any sores and that the herpes test is not very accurate. He also ruled out a UTI and yeast infection. For the itch he gave me flagyl and doxycycline just as a precaution but it hasnt done much to stop any symptoms.

I was wondering if you could explain the painful ********* and the itching to me if you know anything about this?