Certain scenes do make Conan look pretty bad
I'm a Conan fan. But even I admit some of the scenes in Conan O'Brien Can't Stop make him look pretty bad.
For instance, when Matt, Conan, and Sona are joking around. As Conan starts improvising, not saying anything too important, Matt joins in. Conan stops and puts Matt in his place. "When Mozart plays the 88s, you don't sit on his lap and play chopsticks." I don't know, maybe this is just one of many incidents when Matt has interrupted Conan. But to me, it seems like Matt is just trying to be friendly and join in the fun, while Conan wants the entire spotlight.
Also, Conan's reaction after the meet-and-greets. Yeah, he is nice to meet those people. But consider this: Imagine you are one of them. You meet Conan, shake his hand, get a photo taken, and leave with a big smile on your face. Then, about a year later, you see Conan in a documentary, talking about how he didn't want to meet you and your family/friends.
As for other scenes, yeah, I get Conan's sarcastic humor. I like dry wit as much as the next guy. But Conan admits he turns his feelings into jokes. So when he constantly mocks certain employees, they must know there is at least a little truth in his words.