The issue is that is has been fact-checked, and the story is bull. That's the difference. The issue with Trump isn't that he disagrees with news stories, or whatever. It's that he gives his base an excuse to dispose of any information that isn't convenient to them. In practice, this means that if someone quotes any news article, they can just dismiss it out of hand. This is NOT the same as fact-checking something, which every other credible news organization did. Either way, you're dismissing the work of journalists. You don't get to be on your high horse just because you happen to agree with the message of this specific article.
Before saying that the activists are trying to stifle free speech, why not actually offer a solution to the problem you're arguing against? Then we can see who wants more freedom of speech.