He lost the popular vote by millions of votes.True. That said, the popular vote does not matter in any sense other than showing how the country as a whole is pretty evenly divided. If the popular vote (as opposed to the Electoral College) were the deciding factor in the election, the campaigns and GOTV efforts would have been run very differently, and the result wouldn't likely look like it did.
Don't get me wrong, this is very important. The fact that the country was closely split along in an election for historically unfavorable candidates shows just how dissatisfied voters were as a whole with both candidates, and how much work we can do to find common ground—surely there is some: many (most?) people aren't single-issue voters.
(The fact that the Electoral College results and the popular vote results haven't been in agreement is definitely a problems as well, and one that should be addressed. But that's a separate issue, and not the rules the 2016 election was conducted under.)