The popular vote is irrelevant for actually winning - what matters is how states at the margins vote. Look at Michigan. Look at Ohio. Look at Pennsylvania. For the Democrats, Hillary was an unmitigated disaster in all of those areas.
Also, keep in mind that most of the electorate votes against party lines, even if the party were to nominate Satan. She completely failed the margins.
I agree with you but a lot of the troubles that she had were difficult to see ahead of time, especially the email server and the leaks. It's easy to slap on a narrative after the fact but at the time Hillary really was the choice most likely to win the the election. I'm not saying that she didn't do an exceptionally poor job in certain areas but all she needed to do was one or two percent better and there would be the narrative of it being a landslide the other way.
Also, keep in mind that most of the electorate votes against party lines, even if the party were to nominate Satan. She completely failed the margins.