This is a difficult question to answer concisely but I'll give it a go. In brief it's due to the publishing and entertainment industries, and the demographic trends they cater to.
First, we need to clarify exactly what pirates we're discussing. The romanticized child-friendly pirates are based upon the Caribbean Pirates of the late 17th and early 18th centuries. The Golden Age of Piracy.
Then we need to look at the major publications about these pirates.
First, in 1678, Alexander Exquemelin published his account of the careers of several Buccaneers operating out of Port Royal and Tortuga. Most notably Admiral Sir Henry Morgan. The story is filled with vivid descriptions of torture and murder and culminates with Morgan burning the city of Panama to the ground.
It was so violent that Morgan actually sued for libel and won his case. Later editions painted him in the light of an English hero.
The second major publication came about 50 years later in 1724. It was A General History of the Robberies and Murders of the Most Notorious Pirates by Captain Charles Johnson. It told the story of famous pirates like Edward Teach, Charles Vane, and Black Bart Roberts among may others.
Johnson (who may have been Daniel Defoe though many dispute it) took liberties in his text. He fabricated dialogue to create compelling characters and filled in plot where there was no historical record. His pirates were villains, but more sympathetic than the murderous psychopaths in Exquemelin's work.
The book was a smash success, especially among boys. But despite trying there wasn't another pirate success for 160 years.
In 1883 Robert Louis Stevenson published Treasure Island. This was expressly a children's adventure novel marketed towards boys, and it did amazingly well.
The primary antagonist, Long John Silver, wasn't much of a villain though. He was treacherous and greedy, but he didn't want to hurt anyone. He adhered to the rules of engagement and tried to keep his men in line. He was almost gentlemanly.
In 1904 & 1911 J.M. Barrie produced and published Peter Pan & Wendy for stage and page. Captain Hook was another breed of pirate altogether. He was well educated at Eton College and wore - in the words of his creator J.M. Barrie - "an attire associated with the name of Charles II, having heard it said in some earlier period of his career that he bore a strange resemblance to the ill-fated Stuarts. In a word, the handsomest man I have ever seen, though, at the same time, perhaps slightly disgusting."
In the 1950s Disney acquired the rights to Treasure Island and Peter Pan. They created a truly family friendly vision of pirates and piracy.
The Long John Silver portrayed in their films was almost cartoonish and did more to influence our popular idea of pirates than any other source.
The film version of Captain Hook is even less realistic. He was childish, cowardly and temperamental. In the words of a production staffer: "a fop... Yet very mean, to the point of being murderous. This combination of traits should cause plenty of amusement whenever he talks or acts."
By this point the pirate as a real villain was virtually dead. Then, 1967, Disney opened the Pirates of The Caribbean Ride at Disneyland. And the decline continued. Blackbeard, who was one of the most terrifying pirates of his age, now wields a wooden sword on the covers of picture books for infants.
Real history, and even popular culture, have bounced back from this a bit. The true story of real pirates and the world in which they live fascinates people across the world. Still, they may never shake that image of 'fairy tales for boys.'
Sorry for the essay. Brevity isn't my strong suit. Still, if you'd like to learn more two fantastic and easily accessible sources are:
Treasure Neverland by Neil Rennie
&
Under the Black Flag by David Cordingly
If you're interested in more learning more and hearing real pirate stories I produce and host The Pirate History Podcast: