Charity Navigator says on its website that not rating the Clinton Foundation is neither a "condemnation nor an endorsement." It's hardly the only charity not rated by the watchdog. For example, Charity Navigator says it does not rate the Rockefeller or Gates Foundations, because those organizations get their primary funding from the families that started them.
The Clinton Foundation does receive ratings from other charity evaluators. For example, Charity Watch rates the Clinton Foundation an "A" while Guidestar gives it a gold-level rating for transparency.
Charity Navigator put the Clinton Foundation on its "watchlist" in March 2015, after press reports raised questions about foreign donations to the Foundation while Hillary Clinton was Secretary of State. It removed the Clinton Foundation from the watchlist 9 months later, after the Foundation refiled four years of tax information and pledged other transparency measures.
Whether a Charity Navigator rating is significant is an open question. Professor Brian Mittendorf, Professor of Accounting at Ohio State University and an expert in philanthropy, puts it this way:
"A Charity Navigator rating would be something that supporters and/or critics would fixate on to support their pre-existing views of the organization or its founders, but wouldn't really provide new information."
Clinton Foundation takes steps to be rated by charity watchdog - May. 12, 2016