There was something about watching your wife getting blown up by wildfire at the hands of your mother that made one snap. Or crumble, if you fancied being poetic about it, just as the Sept of Baelor did. A magnificent fortress with generations of history and legacy destroyed at the hands of his mother. Likewise, his wife destroyed at the hands of his mother.
Simply put, Tommen decided it was not fair.
He wanted Margaery by his side. He wanted the girl who treated him ever so kindly, who paid attention to him the no one- not even his mother, who had always been so preoccupied with Joffery- had done before. He wanted the woman he had taken as his wife under his cloak and promised to protect and cherish.
Tommen wasn't stupid. He knew that his mother and Margaery were at each other's throats, vying for power over him. But he still loved them both.
But his mother... she killed the girl he loved.
Tommen wasn't completely stupid. Sure, he wasn't the brightest, but what could you expect? He wasn't raised as an heir or a crown prince. He'd hardly been expecting to be anything other than the spare second son until Joffery went and got himself killed.
Expectations were piled on him within the fortnight. He was straddled with the title of the ruler of the seven kingdoms while being challenged by those claiming him and his siblings as incestuous bastards. He was pushed into the Game, never having expected it.
And so, he listened when people like his mother and grandfather told him what to do. Joffery didn't listen when he killed Ned Stark, and the war was started as a result.
He listened to his grandfather when his Uncle Tyrion was on trial, he listened to the High Sparrow when his wife and his mother were condemned, and yet again when he proposed to mile the Crown and Faith, and where did all that end up? With a burning Sept and screams coved by its explosions.
All he wanted was Margaery. It wasn't fair.
He was wholly prepared to give her the world, carve her name on the Iron Throne, and give in to anyone's demands- so long as it kept her by his side. She was so sweet, with their shared dislike of Joffery, with their agreements over how overbearing Mother was... she was so... perfect. So perfect for him.
And his mother saw that as justification to remove her from his life. She didn't want anyone else controlling him but her.
He didn't want anyone controlling him either, he decided. It wasn't fair. And so, after putting his crown aside, he flew.
He hoped Mother wouldn't feel too bad about it, even if she did play a part in his death.