It is true she won a plurality of the votes and leads by a few tenths of a percent in the popular vote, but she never won over the majority.  I believe the number is roughly 47.8% to 47.2%.  Another way to look at it is that Trump won 30 states, Hillary 20.  To me that is more telling and is why we have that "quirk" in the Constitution as a way to limit power of the most populous regions of the country or even several of our large metro areas.  If that "quirk" were to be amended out of the Constitution, so be it.  But then we wouldn't be the United States of America anymore.  We would just be regions defined by beliefs and values, with the middle and the southern parts of the country as one large region separating the West Coast and Northeast regions.
History will show that she was the first woman to get nominated for president.  It will also show she flipped from moderate to progressive, mishandled classified info, took money from human rights abusers, and was a really weak candidate.