At first yeah he's being mean, but later he's more saying it out of affection
He is teasing her when he gives her that nickname. There is a bit of nastiness in it at first because words are the only way he can fight at this point, but there is veiled respect there too because he suggesting she as strong and fierce as a dragon. He would try to bully her and she would meet him head on, wouldn't back down and in the end, got her way. Dragons are hard to fight. Later, when he keeps using it, it is because it has becomes something of an 'inside joke' between them, but it's use is also acknowledging that his success is due the her continued strength and determination. There is nothing but respect and affection in its use by then.
he still calls her dragon lady even after knowing that they were in love with each other? now that's just weird