Black heads? Are they fleshy colored (assuming your skin color is light in pigment)? Do they sort of "go away" when your skin is relaxed and not tightly pulled (e.g. when flaccid)? Are they arranged in an almost organized manner (e.g. a grid of sorts)?
You might be describing sebaceous glands, glands that secrete oil to keep the skin of your penis movable and stretchy. If this is the case, they're probably inflated because you're overworking them. If you masturbate without lubrication often, or if you simply live in a dry climate or eat a poor diet, or if you were born when Jupiter and Venus were aligned, your sebaceous glands will pop out for people to see.
There's nothing wrong with them, nor is there anything wrong with your penis. They're simply working at the capacity they need to, and their size reflects that.
If you want them to go away, try to moisturize the area after you shower, and use water-based lubricants. This should help, but for some people, visible sebaceous glands are just something they've got to live with.
Now, if they're irregularly distributed, the size of a wart, fleshy colored, flat-headed and if they never seem to change locations, that is quite possibly HPV, which case you'll need to visit a doctor for a proper diagnosis and treatment (nitrous oxide "freezing"). Even with treatment of visible warts, the virus will still remain, and you can pass HPV even without an outbreak.
If they're red, painful and localized around a hair follicle, it's probably an ingrown hair. These happen when you shave your penis and scrotum improperly, and the hair tries to grow back, but is prevented from making a straight-shoot out of the skin due to the way it was cut or damage to the surrounding skin. You can't really cure them, they just go away on their own, but you can prevent them by using a fresh razor, shaving after a hot shower or bath, shaving with the grain of the hair, and using a soothing lotion after shaving.
Finally, if they are red, seem to have white heads (much like pimples), and don't seem to go away like pimples do, it may be molluscum contagiosum, a variant of the pox virus. This virus (although spread through human contact, like during sex) isn't really an "STD" as much as it's just a virus, because you can get it from showers, handshakes, used towels and pools. It makes pimple-like red bumps in the infected area, and in most cases goes away on it's on (like chickenpox) in a matter of months or years (unlike chickenpox, which is 10 days-ish). You can have them burned off, but like HPV the virus never really goes away. Overall though, it is quite harmless, just visually unappealing.
In any case, if you're having sexual doubts because of these bumps, you may want to (and really should) see a doctor about it. Assuming the worst (HPV), you'll want to know that you have an infection, but I'm going to presume that it's probably just over-worked glands, and your doctor will be able to diagnose you and ease your mind. Worrying about bumps isn't fun, especially when it's on your most important asset.
