Just recently, a modder decided to tweak some of The Legend of Zelda games. He released this gender neutral mod for the original The Legend of Zelda, as well as for Link to the Past, Link's Awakening DX, The Minish Cap, and Twilight Princess. They're optional, harmless things that tweak dialogue, not touching the original character models or story. It's an interesting thing and amazing how a few alterations could open up the game and character, while also keeping Link who he is.
Sure, questioning the nature of an icon can upset the status quo. People have very strong opinions about characters they've known and loved for years. Which may, in turn, upset the people who might feel threatened by a change, even if it could be a well-meaning one. But the good news is, we have a situation where Link can be whoever the player wants the character to be! Everybody gets to win this one.
After all, Link is an established character. He's been who he is since 1986, when The Legend of Zelda was released on the Famicom Disk System in Japan. Nintendo's been very clear about his identity. It wasn't like it was with Samus, where she had a gender-neutral name and wasn't "revealed" until her first mission was done. Link always bears the Spirit of the Hero. He looks the same across generations. Some may want to argue his gender should remain stable too. In many entries, he even has a family and background that firmly establishes him as more than some avatar people project themselves onto. Which is great, for people who like him as he is. They can easily enjoy the games as they are.
But it's just as easy to say that he could be something more or different. Link has always acted as a blank slate for the player, even when certain qualities are attributed to him in individual games. He's a silent protagonist, which makes it easier for us to consider him our representative in the world. He even has an androgynous appearance, with long hair, a slim build, and a face that could be considered both handsome and pretty. We associate the name "Link" with a man, but it could easily be gender neutral too. That the Link gender neutral mods could be made with so little alteration is also telling. This makes it okay for people who want to personalize Link to do so. Link's an icon, of course, but he's also you.
We even have both male and female representatives of Link now, after all. Which is great for people who want another variation of the hero, but also want Link to always be Link. Hyrule Warriors Legends has given us Linkle, a young woman who believes herself to be the hero, in the same way Link is considered the hero in his games. She has adventures with the Skull Kid, and is even accompanied by Midna for part of her adventure, just as Link did in Majora's Mask and Twilight Princess. Fans have already proclaimed their love for Linkle, and Nintendo could always make her the star of her own games, eventually. Again, everyone gets to win.
There's really no harm to questioning it. The way Link is designed, he can be whoever you want him to be. He's your representative in a world in need of saving. People who want to ponder his identity can, and we now have mods that make that easier. Those who want to savor and enjoy the games at face value can as well, with many entries offering amazing adventures where a stalwart male hero saves Hyrule. This is, fortunately, one of those rare situations where everyone can find a way to be happy, whether it's with the official materials, mods that allow them to customize the game to their liking, or a spin-off that adds one of the cutest heroines ever to the series. There's a Link (or Linkle) for everybody!