He's not so much a racist as he is narrow minded and judgemental. He lumps one group of people together into the category of pirates when in all actuality, every pirate is different. The writers have said that the series is about what makes a pirate and more importantly, what is a pirate. Jack may have a pirate brand, but he's not a true pirate.
His words against pirates stem from ignorance more than pure hatred. How is he supposed to know that there are degrees of piracy when his limited experience involves the attack on his ship when he was a boy?
I would say that if Will despises Jack in AWE, it's not so much because he is a pirate, but because Jack potentially stole the thing that he wanted most in the world.