I don't buy that. One can critique on the basis of analytical thinking without being smug. Smug means "having or showing an excessive pride in oneself or one's achievements." I have worked with many very smart people, including actual (not pretend*) Nobel prize winners in economics, who are more humble than the average Sorkin mouthpiece. This is what grates. Sorkin sets his characters up to be "the smartest person in the room" without the humility that truly smart people have of understanding that they can't know everything and always be right. And then, more often than not, the characters' arrogance is shown as justified because, lo and behold, they were right (as the storyline played out).
*ETA: Making Jed Bartlett a Nobel Prize winner was typical Sorkin overkill. He couldn't simply have been an economics professor turned politician. No, Sorkin had to put the sheen of Nobel on him (smart! smart! super-smart!), which was kind of ridiculous.