I can't judge whether your pain is due to urethral inflammation (urethritis), minor trauma from the swab, both (ie, swab not causing pain but making it worse), or none of these. Certainly passing the swab into the urethra is painful for many men. Whatever is going on, it almost certainly isn't an STD, given your sexual history. Otherwise, it is hard to speculate. If you worked something irritating into your urethra during masturbation or just washing - especially soap - that might explain it.
Most likely the pain will just fade over the next few days; if it doesn't, discuss it with your doctor. And by the way, if the pain is due to the swab, it doesn't mean your doc did something wrong. Some men just have painful reactions to urethral swabbing.
Good luck-- HHH, MD
How come dr. skipped my question and answered one that was posted after mine??
I think it is highly unlikely it is herpes if the urethra. That would be more than "irritating", It would be excruciating.
And I agree that it can't be NGU from protected sex 6 months ago. I think it is nothing and will go away. I have had it before. It will clear up on it's own. I went through every test in the book...nothing.