Basically, the truth is what I always feared, which is that there were a ton of what I called "closet Trump supporters" out there who were unnaccounted for in the polls. These were not the people who would have daily pro-Trump or anti-Clinton Facebook rants, or the people who boasted about their support for Trump to friends or in the workplace, or the thousands of people who attended each of his rallies.
Rather, these were people who were embarrassed to admit that they planned to support Trump -- even to the strangers who conducted these polls. Polling, in general, is rooted in the belief that the people participating in these polls are being completely honest, which is obviously not always the case.
Beyond that, there was the surprise resurgence of the FBI "investigation" into Clinton's emails (which wasn't even really a re-opened investigation). There's no telling how much of an effect that bombshell had on the election that was to take place only 11 days later. Despite the fact that it amounted to nothing and was announced to be a "false alarm" days later, the damage had already been done, it still led to bad headlines for Clinton leading into the election, and definitely might have been the "straw the broke the camel's back" for some people who were on the fence or hesitantly leaning towards Clinton at that point. Trump latched onto it hard, and he wound up having a surge of momentum right through Election Day.
But even when the polls were showing a tight race between the two of them, most people just couldn't even fathom that Trump actually had a chance of winning it. The narrative was always that Clinton had it in the bag, either by a landslide or in a fairly tight race.