I agree with Onyx, it's hard to protect your kids from things that you consider a bad influence. If you are very opposed to pirates though then it's reasonable that this is not the theme for your son's room, and when he is older and still shows an interest you can do as others suggested and explore the real history behind them.

Personally I was opposed to The Wiggles on the basis of crimes against music, and I managed to avoid any Wiggles influence in my house, so it is possible to stop a particular theme of play from being in your house.