A lot of these global rankings are ultimately based more on research and publications. The size of the institution is a factor. UVA has not been a relative powerhouse in STEM graduate study and research. Schools that are lower ranked in USNews undergraduate education, like Texas, Washington, Illinois, and Wisconsin are larger and focus more in this area and research, and consequently rank higher in these types of rankings.
Very few universities are strong across the board (undergraduate, graduate professional, research, graduate science, graduate humanities). You might cite Stanford and Harvard as being in this category (although even Harvard might struggle in engineering). Among publics, Berkeley is sometimes mentioned, but I would honestly question their undergraduate commitment. The rest have to choose where to focus. UVA has focused more on undergraduate education than the typical flagship public university and has excellent schools of law and graduate business.
Anyway, prospective students should focus more on their area of study. Dartmouth, for instance, is also not ranked very high, but they provide excellent undergraduate education. You could say the same of William and Mary.
As someone else pointed out, some of these rankings, like the Times, I believe, include criteria like percentage of international students. I think this is arguable at best and probably introduces some bias in the outcomes (e.g. it helps Oxford and Cambridge for instance rank higher).