Your symptoms suggest the possibility you acquired gonorrhea, chlamydia, or nongonococcal urethritis (NGU). I can't tell from your question whether there was unprotected penile-anal exposure; if so, another possibility is a bacterial urinary tract infection. However, the tests you had would have reliably diagnosed all of these. And in case the tests missed something, the ciprofloxacin would have cleared it up; if you had one of those infections, you don't have it anymore.
Herpes rarely presents only with painful urination; almost all symptomatic cases would have obvious external gential lesions. so your persisting penile pain almost certainly isn't herpes.
Pain/discomfort often continues after an infection or other injury has healed by all objective criteria. For example, people often have continuing pain in an ankle long after a sprain has healed. Continuing penile discomfort doesn't necessarily mean an ongoing infection. I suggest sitting tight; the pain probably will gradually fade. But if it gets worse, or if it doesn't go away over a couple of weeks, follow up with your health care provider.
Good luck-- HHH, MD
HHH, MD