Yup.
I don't know what he's confused by because it's pretty simple.
When you see so many acts of bigotry, racism, and other randoms acts of hate happening around the country, then it's an obvious sign that many many people in this country on both sides of the fence have a perception of him.
That rapidly growing perception of him is a negative one, and because it is a perception shared by so many people from different walks of life, he has a responsibility to distance himself from it since he is the president elect of the United States, after all.
And let's not pretend like he can just wipe his hands clean of this either. Just because he didn't tell anyone to do these things or condones them doesn't mean he's blameless either. His behavior throughout his campaign is the reason why so many people view him in the light that they do and now he has a responsibility to clear some things up and take a stance.