Pirates flags were an powerful pop icon at 20th century, and still are. A common denomination to pirate flags is "Jolly Roger", usually represented by a black field with white skull and crossbones. But it differs a bit from their historic origins.
A common pirate flag from Golden Age of Piracy (16th century) is a plain red flag (Qatar and Bahrain put white on their flags to prevent retaliation to their ships). Some histories, possibly untrue, relate that the term "Jolly Roger" comes from "jolie rouge" ("pretty red" in French). The reason is curious: in naval code, a black flag means there're prisoners at ship; a red flag means there aren't (in pirates' case, all the enemies are dead). Click here to see an authentic red Jolly Roger.
Along the time, the black flag increased of use. The color was chose because it doesn't resembles any national flag, suggesting pirates are people without homeland (similar symbolism explains the use of black by Anarchists).
Now a final explanation: skull and crossbones are commonly used by pirates, OK, but not a lot more than full skeletons, hourglasses, cutlasses and "pierced" hearts. They're all used as symbols of danger and experience.
So, if you constructed a pirate flag in your childhood, I sorrily advert you were mistaken. But children like fantasy, however.
And, in the end, a very curious Jolly Roger, from Bartholomew Roberts, showing a supposed encounter between him and the Death: