Before McCallie, I had always gone to public school in a tiny Georgia town(Hiawassee), so switching to McCallie was a big deal, and a big change. There were definitely some of the things the NYTimes article describes: lots of money went toward athletics and athletic facilities(the US women Olympics crew team trained there), there were children from families of the ridiculously wealthy(most of whom were very nice, polite, and never snobbish), and by the time I was graduating there was a huge new dining hall/conference facility that had been finished, and plans for a state-of-the-art dorm building underway.
But I don't think McCallie misspent their money on those things, at least not in relation to how they spent on other things. Athletics never over-shadowed academics. Most of the teachers I had at McCallie were better than most I've had in college, and I don't know of any public school where I would have been able to receive 5 semesters worth of credit for English classes my senior year. McCallie had a great music program, and didn't skimp on funding for art classes either.
While I was a student, I never thought about the size of McCallie's endowment or how it was used, possibly because I never saw any indication it was being misspent. Now, Wikipedia tells me McCallie's endowment is ~$60 million, and that 85.7% of their expenditures in 2007 went toward program expenses. That sounds pretty good to me.
More importantly, the stats on McCallie's own site confirm what I saw among the student body: http://mccallie.org/Internet/Default.aspx?pid=336 Almost 20% of students receive financial aid, and there are 55 students receiving merit scholarships this year. At a school where the total enrollment is just over 900, that's a lot of kids who would find their abilities wasted in public schools being given great opportunities.
Sure, "never let schooling get in the way of your education," and other Mark Twain wisdom. But not all prep schools are just comfy surroundings and a well-known name for rich kids to pad their college applications with. Some of them are really great tools that give, and encourage seeking out, a great education.