When Nala says 'I thought you were very brave'...

[nathalie]

The animation that goes with it, would be pretty rude if it were sarcastic, so no, just look at Nala when she says it.

[MoBeh]

[SimbasGuard]

[Meskhenet]

She was being sincere. Given what they both had been through and Simba feeling disappointed that his father was angry at him for disobeying him, Nala was reassuring him that he was brave for protecting her from the hyenas even when he was just as much in danger as she was.