Awhile back I remember a critique of the third Pirates of the Caribbean film that takes issue with, among other things, the depiction of pirates as some kind of quasi-ethnicity being mass-murdered by the East India Company. In particular, the reviewer objected to the sequence where a bunch of pirates, including a child, get hanged and it's depicted as a bad thing. After all, pirates are basically sea robbers and were prone to committing atrocities--for a paper I did on the historiography of Atlantic piracy, I found accounts of pirate Henry Avery's men committing a mass rape of Muslim women on the pilgrimage to Mecca, other pirates torturing and murdering the crew of a ship they'd taken, and various other grotesque acts. The book Under the Black Flag strongly disputes the romanticized view of pirates that omits or downplays their bad behavior.
However, there are pirates and there are pirates. The earliest buccaneers weren't pirates at all, at least at first. They were European adventurers who lived in various Caribbean islands, hunting the cattle that the Spanish had introduced (that had gone wild) and selling the meat to passing ships. Their name comes from a Taino Indian word for "grill." The Spanish repeatedly tried to run them off, until they took control of the island of Tortuga and started attacking the Spanish instead. Furthermore, many later pirates were actually licensed by their governments to attack enemy ships in wartime. The "classic" (and worst-behaved) pirates were at the tail end of the age of piracy, when governments no longer employed freelancers against each other and the pirates basically preyed on everybody.
(To be fair, many pirates had understandable reasons for adopting that way of life--sailors who'd been abused aboard merchant ships or in the military, runaway slaves, etc. Marcus Rediker's Villains of All Nations and the book he co-wrote The Many-Headed Hydra describe these people in more detail, including accounts of how sailors on ships attacked by pirates would often jump ship and join them. However, that still doesn't acknowledge torturing people to find hidden money, rape, etc. Somebody can have a sympathetic back-story and still be an unpleasant, nasty person. Consider Severus Snape, the poor Goth kid oppressed by the rich spoiled popular athlete as a student--who became a cruel teacher who bullied his students and rarely if ever bathed. And Snape is one of my favorite characters.)
So here's a way to get sympathetic pirates and still be at least somewhat realistic. Depict Jack Sparrow and others like him living on some nominally-English but de facto independent island near Port Royal in Jamaica, perhaps a more benign and less violent version of Nassau (depicted as an independent pirate commune in The Republic of Pirates). Emphasize that despite the disdain of Port Royal's residents, most of them are making an honest living selling meat to passing ships, fishing, growing enough food in a month to sustain them for a year, etc.
If they are engaging in criminal behavior, it's more sympathetic activities like smuggling to avoid excessive tariffs. After all, our Founding Fathers did it. :) If there's any actual piracy, it's defensive or retaliatory in nature--they're fighting more violent criminals trying to take control of their island (think how The Godfather made the Corleones sympathetic by pitting them against even more immoral crime families and dirty cops), plantation types trying to reclaim members of their community who'd fled slavery, former employers who'd mistreated them, etc. Emphasize the more sympathetic parts of Jack Sparrow's back-story in particular--according to a deleted scene, he refused to participate in the slave trade. Think Han Solo, who on the surface was a rogue, mercenary, and criminal but had been drummed out of the Imperial Navy for defending a Wookiee slave.
However, not all residents of this island are good folk deep down beneath the veneer of roguishness and petty criminality. Barbossa could be present as a crueler and more violent pirate, with the back-story of him usurping Sparrow's ship still there. He comes to the island and despite Sparrow's opposition is welcomed for his wealth and powerful ship. Then he promptly starts raiding the Port Royal merchants, engaging in the more typical pirate atrocities (including the "dining with the crew...and you'll be naked" implied rape threat from the first film). The fantasy elements can stay or not--their terrorizing her with their undead nature would further show they're bad apples and retain the supernatural stuff depicted in the Disney World ride.
While all this is going on, we can have the canonical romance between Will Turner and Elizabeth. Will is an unappreciated apprentice--he's a trained sword-fighter and makes an excellent weapon, but his lazy master gets all the credit. He might be tempted to join the pirates himself. Elizabeth could too--she clearly has issues with the gender roles of her time ("Do you like pain? Try wearing a corset!") and isn't interested in marrying the older Commodore Norrington.
For the later films, here's where the East India Company (or a more Caribbean-focused equivalent) comes in. Even with Barbossa defeated, the Powers That Be use the fact that Sparrow's island hosted him and many of the inhabitants joined him as a pretext to drive the population away...so they can make it into a sugar plantation. And sugar-production back then was horrifically destructive to the enslaved work force. This is where we can meet Beckett and get his back-story with Sparrow. If Sparrow and his friends engage in outright piracy and the more aggressive behavior originally more characteristic of Barbossa, it's in defense of their homes against a ruthless and dangerous opponent operating under the color of law.
(And, if we retain the fantasy elements, possibly in collusion with evil supernatural forces like Davy Jones.)
So, you all like?
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