The reasons for saying yes are two historical moments, one well known, and one less known:
The first one deals with the French Revolution, during the Reign of Terror. Specifically, I am referring to the Law of 22 Prairial that was created by the Committee of Public Safety. For those who don’t know what I am referring to, it simply was that if anyone was accused under the purview of revolutionary justice, the Law would allow the Committee to indict and persecute said, individual. While the individual would be able to defend themselves in a limited way, the committee would ultimately give the only punishment…death. Basically, if you were accused of being anti-revolution, supporting the old ways, you would disappear in the night, be held for trial, then executed.
False DMCA claim
The second less-known historical event, which relates directly to the question was the false DMCA claim filed by VenomFangX (VFX) against ThunderF00t (TF). For those who are unfamiliar with this story, it basically starts off with two different individuals. VFX was a Creationist, who challenged world views that worked against the Bible and tried to demonstrate that the Bible was correct, often using science to support his claim.
TF was another personality, who spent his time debunking his claim, and soon others claim in the video series, “Why do people laugh at Creationist?”. Both become popular within their own respective groups, though TF was having more popularity than VFX. VFX believed at first that his faith would allow him to dominate, and when that did not work, he resorted to smearing campaigns. Once again, when that didn’t work, he set himself to filing DMCA.
I recall that TogetherforPeace (TFP) (whom I have much respect for) told his part in this, where he was given a list of videos by VFX who felt violated his rights. TFP returned a list of what he said did violate his rights (not one of them containing TF videos) but warned that he should be careful as there are consequences for filling false DMCA. It appears that VFX ignored this warning and filed the claim against TF.
VFX felt God was on his side and felt that he was untouchable, though at first, he denied that he did file and that a “friend” did it. TFP revealed private messages between himself and VFX demonstrating that VFX did indeed file those claims. TF initially gave him an ultimatum in which he could face legal action, or to have his account closed for a year, but instead took the high road and told him to upload a video in which VFX reads a prepared statement, where he admitted to wrong-doing and apologized for all his mistakes relating to the filing of false DMCA.
Now this is just a brief overview of it, but you can see that VFX had intent, he wanted to take down Atheists who disagreed with him (as there were others besides TF). He cared not for the legality of what he was doing or any other sort of harm he might be doing and instead only that he might take down his opponents.
YT in the past would simply take down videos accused of DMCA without really investigating it. Likely VFX knew this and thus filed away knowing it would take down videos and possibly accounts.
This ties into the French Revolution because it was easy to accuse your neighbor that they were anti-revolutionary and they disappear in the middle of the night, never to be heard from again. YT acts almost like the Committee of Public Safety and VFX acted as a citizen who took the opportunity to cast out a rival. This classifies as a Hate Crime because the motive of VFX was against the victim’s (in this case TF) affiliation to him being an Atheist. Hate crime has little to do with the emotion of hate, rather pertaining to attacks against a person for race, religion, sexual orientation, disability, ethnicity, etc.
This needs to be seen as a hate crime because theists who engage in filing false DMCA because they are unable to win in a debate against their opponents, do so to let them disappear in the night and never be heard from again so the only word that remains is their own. This has happened many other times by theists against Atheists, that rather than debate their opponents, it is easier for them to disappear. If the reverse were true, then it would be the theist claiming that filing false DMCA was a hate crime.
Why is it, what is good for one bad for the other? Should it be, what is good for one is good for the other? Or do we simply ignore anything that is against atheism simply because they are different, and in history, differences were always hated and feared? No matter what your personal feelings may be, you must concede that trying to hurt someone for being something they cannot directly control is wrong and is by that very definition a Hate Crime.