TL;DR version: The campaign strategies of Trump and Clinton were designed to win the electoral college, not the popular vote, so a discrepancy between the two is not remarkable or significant.
The article.
My summary:
* Clinton didn't campaign in Texas because she knew she'd lose that state
* Trump didn't campaign in California because he knew he'd lose that state
* Neither campaigned in Michigan until the state began to waver towards Trump
This means that both Trump and Clinton didn't try to win the popular vote, and both of them walked away from popular votes in California and Texas. It's unreasonable to re-interpret the vote -- after the fact -- as being unfair.
On a personal note: in Chicago, the Democratic machine is so deeply entrenched that the Republicans didn't even bother to run in almost all races. And the Democrats won all the races. As such, its not unreasonable -- under Electoral College rules -- for Republican voters to not bother to show up.
I happen to be a fan of the Electoral College system of voting, as it means that the candidates have to appearl to wide swaths of the populace instead of just city slickers -- but that's an argument for a different day.