that ranking system is probably based mostly on research, funding, academic resources, faculty, etc., and takes into account all the different schools within the universities (undergrad, grad, professional)...cal has all that...if you take a look at grad school rankings, cal is in the top 10 in damn near most programs (just like harvard, stanford, and mit)
the other rankings you more commonly see are more undergrad-centered and based more on admissions selectivity, quality of undergrad education (class size, etc.), financial aid, in addition to some of the other factors mentioned above