As I have said before on this forum, when it comes to interpreting skin/genital lesions, I cannot compete with the diagnosis or opinion of a health care provider who has examined you. If he said they aren't warts, take his word for it.
As Sarah C. says, pearly penile papules sound possible; they occur around the edge of the glans (head) of the penis. If along the shaft, these are less likely, more likely sebaceous cysts. In any case, you can be confident they aren't an STD and have no important health implications for you or partner(s).
Thanks for your kind comments about the forum. Good luck--
HHH, MD
Most men have small, light coloured bumps on their penis and scrotum - they're called pearly penile papules and are very very normal.
Doing a websearch for "pearly penile papules" and reading about these very normal little bumps might help put your mind at rest.
Cheers,
Sarah_C