The NY Times column links to my website, and I was one of the people interviewed for the piece. Although the website does emphasize the quality and benefits of public honors colleges and programs, the site is independent. Personally, I believe that a young person who has visited and really felt comfortable at HYPSM, Columbia,etc., and whose family can finance that option with or without need-based aid, should by all means enroll at one of those wonderful universities.
But most applicants, even those as bright as those actually accepted to these elite schools, are denied entrance, often because the schools have so many priorities in addition to academic ability. And our research shows that, given a cohort of students in the top 8-9% of SAT and ACT scores (~1300/29), there are not enough slots at elite private universities and liberal arts colleges, or at UCB, Virginia etc., to accommodate these students.
So what happens to the rest? Well, public AND private honors colleges/programs are a very strong alternative. And the public honors programs, in general, will cost less out of pocket for many two-earner families. Here is a somewhat nerdy post we did on the subject of elite slots across the country. http://publicuniversityhonors.com/2015/06/16/4770/