Because the primary criterion for a high rating on the list is the measured (by me) desire of students posting on CC to attend the school. MIT (along with Caltech) is a strong competitor to HPYS when it comes to this criterion.
Also be aware that the prestigiosity rankings, while of course an entirely legitimate and scientific ranking system, also serve as a commentary on ranking systems in general.
For lazy people, below are the most recent prestigiosity ratings (in milliHarvards)–I haven’t seen anything in the most recent discussions to suggest changes:
Harvard: 1000 mH
Yale/Princeton: 998 mH
MIT (or Caltech): 997.365782322119 mH
Stanford: 995 mH (998 west of the Mississippi)
Penn (Wharton): 992
Duke: 990 mH (995 south of the Mason Dixon line)
Columbia: 990 mH
Williams, Amherst, Swarthmore: 988 mH
Brown: 987 mH
Penn (other than Wharton), Dartmouth: 985 mH
Cornell (CAS and engineering): 980 mH
Chicago: 980 mH
Northwestern, WUSTL, Rice: 975 mH
Johns Hopkins, Vanderbilt, Emory: 950 mH
Tufts, Georgetown, Wesleyan, Middlebury, Bowdoin: 925 mH
University of Virginia: 900 mH (950 in Virginia; 990 in Virginia excluding Northern Virginia)
UC Berkeley: 900 mH
Michigan 890 mH
UCLA, CMU, Notre Dame: 880
CC Darlings (in alphabetical order):
Alabama (for merit scholarships)
Carleton
Claremont Colleges
Deep Springs
Grinnell
Harvey Mudd
Kenyon
Macalester
Oberlin
Reed
Smith
St. Johns