What can cause urethra pain in a mail if he has had tests showing no abnormalities and has taken cipro (ciprofloxacin) and his culture is now negative.?

Complicated. He should seriously consider seeing a urologist. Although probably harmless and something that will resolve with time and good diet, this could be something more serious that needs to be treated. Meanwhile, continue using condoms, even though the tests are "negative". Always play it on the safe side; you don't want to play ping pong with chlamydia, an infection that can affect your fertility.
Lots of things. Pain in the urethra can come from bacteria that don't show up on typical cultures. Prostatitis can also refer pain to the urethra.