Firstly, it has to be noted that overall rankings, by definition, paint a very rough picture due to averaging universities' key performance indicators (KPIs) across a variety of disciplines and fields of study. Since both Russia and Israel have a rich history of scientific achievements mostly in hard sciences (mathematics, physics, etc.), the overall nature of world rankings introduces a significant bias due to considering the above-mentioned whole spectrum of disciplines and fields of study. If you would consider a ranking in a particular discipline or research area, where Russia and Israel traditionally have powerful positions (i.e., computer science), the situation would be significantly different, confirming those positions (as have been already mentioned in some comments above).
Secondly, if you would pay attention to methodology used in, for example, QS, Times and CWUR rankings (see this page, this page and this page, correspondingly), and compare QS and Times indicators with CWUR indicators, you would notice that the former assign a high weight on some factors, which IMHO are quite subjective and biased, whereas the latter represent a much more balanced set of indicators. In particular, I'm talking about assigning 40 percent to academic reputation (QS) and 24 percent to academic reputation and research income (Times), where reputation is determined by surveys (thus, subjective) and research income is unadjusted for geo-economic differences (thus, biased; even the methodology itself labels that indicator "controversial"). On the other hand, the CWUR ranking contains a balanced set of indicators, all of which are objective measures. Therefore, while you call CWUR ranking "an exception", I would argue that it much more fully represents real life situation, whereas QS and Times do not.
Thirdly, there are other country-specific factors, which existing methodologies do not include or adjust for, which bias the results of rankings, which represent the situation very approximately in the first place. I mean such factors, as underfunding (as noted by @xLeitix), administrative issues (i.e., bureaucracy), economical issues (i.e., corruption) and political situation in Russia, which generates more than usual "brain drain" (thus, introducing additional bias) as well as [public] underfunding and geo-political situation in Israel (I'm less familiar with this country's research environment, so this is just my best guess, based on what I know and some common sense/logic).