Isaacson did not paint a rosy picture of Jobs. Isaacson's indirect conclusion was that Jobs was a complex personality that a displayed wide range of traits and emotions.
As far as him allegedly firing employees because he didn't like the way they looked, perhaps Isaacson couldn't substantiate the rumor and that's why he didn't included it (IIRC). But, there are plenty of OTHER stories of him being a jerk, including parking in the handicap zone with a bogus/missing license plate. (A joker employee put up a sign in that spot saying, "Park Different".)
And his storied relationship with his daughter could be for a lot of reasons, not just money. Based on interviews with friends and family, speculation was given that Jobs felt abandoned by his genetic parents and this somehow left a deep psychological scar on him which he may have projected onto his daughter. Some suggest that this feeling of abandonment is partly what drove Jobs to "prove to the world" that he was worthy of "real parents".
He was not materially externally flashy most of the time (relative to his wealth), although he was interested in custom designing a big-ass yacht when he found out he was dying. He was quoted as saying he picked that big personal project partly to distract him from his pain and approaching death, if I remember correctly. He needed goals to keep his mind off stuff he didn't want to think about; another clue to his drive.
But yes, he was cheap at times. But being cheap is not "greedy" in the usual sense, except maybe as a symptom of greed. Some say it was a game with him to test the limits of what he could get a way with. Thus, it wasn't the money itself, but the pleasure of successfully manipulating using money. He did seem to get pleasure in toying with people, which his pranks with Woz fed in to.
From a personal level, yes, most would consider him a "big jerk". But genius is not measured in personal popularity.