Fitzgerald has come in for criticism after McIlroy damaged his wrist when he opted for a risky shot that resulted in him hitting a tree root on Thursday.
Pundits have suggested that Fitzgerald should have given the 22-year-old better guidance and advised him not to play the shot as it could have resulted in a career-threatening injury.
"He's my caddie, not my father," said McIlroy.
"Hindsight is a great thing, but looking back it was a mistake in judgement. I thought I would be able to get away with it.
"I feel as if I can make birdies out there. If I don't think I could contend I probably wouldn't be playing. And if it wasn't a major I probably would have stopped yesterday."
McIlroy played with his wrist bandaged on Friday and ended the day three-over par at the halfway point.