Disclaimer: I do not own a thing minus the plotline.
Blair Waldrof had a lot of problems. The main two consisted of her best friend and her on/off again boyfriend.
The problem she had with Serena and Chuck was the same. They were both too perfect.
Serena was perfect because she did everything with ease and grace and never had any flaws to cover. She was everything Blair wanted to be and everything she tried to be; only to fail miserably.
Her problem with Chuck was he never tried to cover his flaws and in that way they ceased to be flaws. Blair attempted to do that as well only for her flaws to become even more visible. Blair hated that no matter how much Chuck Bass cheated smoked sinned; he would still always be better than her. And no matter what she did one fact would never change: He was in love with Serena Vander-woodson.
So yes Blair Waldrof had many problems but those two never ceased to be her main one.
Did she hate them?
If she answered honestly the answer would be yes. She hated them for being perfect together and apart.