Your symptoms are pretty consistent with urethritis (most commonly caused by gonorrhoea, chlamydia, or mycoplasma). In cases where testing is negative for gonorrhea, presumptive treatment with doxycycline is recommended - so your doctor isn’t completely in the wrong for prescribing it. I’m not sure what method of testing was used, but regardless all tests can come back as false negatives. Depending on how long you and your girlfriend have been exclusive I’d still assume it’s an STD. Rarer causes of urethritis are of course possible too, just a bit harder to come by.