alt Hacker NewsPro guitar teacher here with over twenty years of experience teaching the guitar, and close to fourty years of experience playing the guitar. I still struggle with properly tuning my instrument by ear. Nothing wrong with my ears. It's just not easy to do this right.
For me it's hard because of tempered tuning, so each string should be slightly out of tune for everything to sound good. If I tuned by ear, I could get two open strings to match, but all the fretted notes and chords wouldn't sound good. On my ukulele I even tune one string down on purpose to make the fretted note sound better. And then there is the inharmonicity of overtones, and some strings have more noticeable overtones that influence how the pitch is perceived.