I have a few small red dots/bumps on the shaft of my penis. They don't hurt or itch. There is no discharge either. They did flare up after I had unprotected sex with my girlfriend. I masturbated later in the day however and they didn't seem to flare up or even get irritated. I've never had an STD and neither has my partner. Really unsure on what it could be

If those dots were itchy I would say it is HSV2, I would go to the doctor for a check up.

Yes, that is very well a sign of a STD or another infection.
You are best if you have it checked.