Arthur had called him worthless, and before he might have believed it. But now Merlin knew better. If his hide was really so worthless, Arthur wouldn't have lied to his father to protect it. He did care.
Merlin had been wondering, when it came down to it, what Arthur would choose: letting Merlin live, or keeping his word to his father. Now he knew.
Before he had kept his secret from Arthur in fear that his prince would have him killed.
Now, he just kept quiet in order to respect his best friend's wishes.