Yes, but because she could not win the votes of a group of testaments to the devastating mental effects of inbreeding, she lost.
Which is why Clinton winning the popular vote is only a demonstration of how the Electoral College is massively flawed. I'm curious what the numbers would have looked like if the votes were distributed proportionately to the popular vote as opposed to the all or nothing system that I think I'm safe in saying has proven itself to advantage the Republicans after two Republican presidential victories in my lifetime that lost the popular vote.
Of course, my point was that saying it was close isn't as much of an argument as it was for Bush and Gore. Now, granted, I am not saying that the Electoral College is the only factor in Trumps victory (of which I give the most blame to the media for treating him with kid gloves while constantly harping on the fucking e-mails), but I do think it is a factor.
EDIT: Also, low voter turnout is not why Trump won, by the way. Turnout was down from 2012, but by only 1.3%.