I don't think the rebuttal makes a fair characterization of Stewart's article. Slate's argument comes down to "Stewart is taking his eyes off the prize, asking us to focus on the 9.9% when the 1% are really the problem" but I didn't interpret the Atlantic piece as implying that those at the very top are innocent in all this. It was more saying that the upper class (9.9%) have been complicit as the top 0.1% have garnered an increasingly vast portion of wealth.
Stewart is asking those in the 9.9% to be more cognizant of those below them, to stop looking up at the 0.1% and realize that the actions they take to improve the outcomes for their children are reducing income mobility.