He's trying. He's only wanted you, his son, to have at least a semi-normal life. To not end up like Jason Todd or even Damian. He's tried to shelter you, the way he believes a father who is a vigilante at night should.
He's spoiled you, but also disciplined you. He's been asking Clark (begrudgingly) for advice on how to be a better dad. He's even let you walk around Wayne Tower, surprising enough. The least to say is, you're his favorite. He's held you up on a pedestal since you were adopted (legally) when you were no more than 9 months old. He's bought you suits, and even skirts (with a couple questions), he's bought all your things without you having to worry.
But you were still worried. He was terrified. You just threw a curveball at him. All it took was six simple words, he'd never thought he'd hear: "I want to be girl," you said with such seriousness and fear, it almost made him nearly faint.
Of course, he'd never throw you out or not love you. He just didn't understand. "You... what?" He asked, no more than a whisper. What hurt the most, was the fact you seemed... scared, of his response.