Batman is not afraid of meta-humans.
Watch this movie and notice;
When Batman is fighting super-powered meta-humans he demonstrates a cool disdain as he casually takes them down one by one.
But when Katana and other Martial Artists challenge him he becomes MUCH more wary and on his guard.
Simple reason; Batman always learns of his enemies AND allies weaknesses in order to stop them should any go rogue. Then when he is able to neutralize the meta-power they tend to be easily taken down as their fighting skills tend to be inferior because they take their meta-powers for granted too much.
But Martial Artists cannot be neutralised in such a manner. He can only study their moves and learn their patterns, something a GOOD Martial Artist attempts to change periodically, rendering them less predictable than Meta-Humans.
So that's why Batman demonstrates open contempt for his empowered adversaries in this movie while equally showing healthy respect and caution with fellow Martial Artists.