I know at the last two institutions I have been, top level administrators seriously consider the impact of any decisions that they make on their US News rankings. I have heard the rankings used as a reason for everything from reorganizing departments in colleges (to shift where certain numbers are counted) to raising tuition (to buy more faculty to lower student/teacher ratio). The problem is that these schools are trying to hit a secret moving target.
Plus, and I think the article said something about this, US News boils something as complicated as a university into one number. We have realized that you can rarely boil an individual student down into a GPA or ACT/SAT score, but here US News is doing that for a whole university. I can look at schools in their forth tier and know that they have some top tier programs within the university. The only slightly fair thing they could do would be to rank all colleges by undergraduate programs (like what they do with graduate programs), but that would be a methodological nightmare and they could probably not fit all of that data into a single magazine.