I don't know how you can look at media organizations like the New York Times and not see that they clearly have a comically overt agenda in how they talk about him and represent his positions.
NYT certainly has a known political bias, and that's no secret to anyone paying attention. Trump highlighting this bias and addressing it would not be a problem. Trump hinting at using state coercion to influence the content of NYT reporting is a huge problem and runs directly contrary to the 1st amendment (not that his presumptive opponent doesn't have her own huge flaws in that department) and US free speech culture.