Bruce is always angry at Clark for everything, being good, doing something stupid, ignoring him, sacrificing himself for the greater good, etc....
Slash mind aside I think Bruce loves him like a brother, when you are close to your siblings you always fight with and are annoyed with them for whatever reasons but you secretly like them and want them to be ok.
I am looking at this from my own experiences anyway, I have a way too perfect older brother that everyone loves and he is just perfect at everything, nice and good and I can't help but being irritated with him for that, still I secretly enjoy spending time with him and think he's a great brother.