Darn. That's quite hard to deal with. I am sorry you are going through that. 
I wish I had some first-hand experience to share with you, but as you know myself I have been pretty shy to make my own videos and stuff.
Trolls look for reactions and any sort of acknowledgement so don't give them that. Don't mention the situation in your videos, don't engage with them just try your best to ignore them.
Another thing that comes to mind is to check out Rebecca Black's vlogs. I am sure you probably can remember the fiasco on the song "Friday" that the internet labelled as the worst ever. She had to deal with a lot of crap and harassment that no doubt still follows her so whatever tips she has to offer on the matter are very well worth consideration.
I think right now, it might be best not to read the comments in your videos if you know the majority are going to bring you down. At least until this calms down.
The best tip I've received about it is that it is out f our control what people think about us. accepting some people will think bad things about us that is not intrinsically good or bad, just what happens we all have people we like and dislike and we have at some point claimed to dislike someone we don't know based on the what the media says. We choose to dislike the projection, the shell we have of that person and just like that the trolls you have are hating the projection they constructed based on whatever video the atheist used to mock you.
I hope it all gets calmer for you in your channel soon. I am sorry you have to endure this. >_<
It's difficult because sometimes it does hurt. And unfortunately, it's a bit harder to ignore because it's comments on your YouTube channel so you can't really avoid the site. If you want, you could disable the like count and the comments but personally, I think that just lets them know that they have won and got to you. It's difficult but the only thing you can try to do is to ignore the comments and focus on the good ones.
Responding to trolls is like giving a puppy a treat when it behaves badly. It's best to just not read them if you can. It'll blow over when they get no response.
Hope things are better for you since you posted.
I usually block, I'm usually bad when it comes to responding to flamebait, so I just do the easy thing and block. For people who bypass that, well, I'm not sure 
I usually block, I'm usually bad when it comes to responding to flamebait, so I just do the easy thing and block. For people who bypass that, well, I'm not sure
I've actually blocked a member of another forum in the past. The guy was insufferable. He was replying to every single post I made, but wasn't breaking the rules. He was deliberately trying to get under my skin. I unblocked him after a time, and now he doesn't bother me. I guess he just figured that I'm not bothered and skip his posts. Most people who try to troll me don't get to me, but I guess there's always that one personality that will make you go ARRRRGGGGGH! from time to time.
There is no way around it
We will must have to ignore them and leave them be. That will get bored of it soon
