I honestly don't see why there should be a difference between atheism and any religion in this regard. All camps will have people yelling loudly. It's just how it is.
This is exactly as invalid as the arguments that hateful Christians aren't "real Christians", or any similar idea.
Here's an anecdote taken from my own personal life.
I don't believe ghosts exist. All of my relatives, however, do strongly.
This is often discussed openly, when I am present. Oftentimes someone will point a statement or question towards me.
Yet, still, if I ever speak about my disbelief in ghosts, the room goes deeply serious and everyone starts acting like I tried to throw them under a bus. They are allowed to freely express their belief, but my opinion is not allowed because it is not in favor with the majority of my family.
If this was about Christianity, instead of ghosts, damn right I would hate Christianity. Reasonable? No. Strong emotions like those rarely are.
That, I imagine, is where a lot of the animosity comes from. Though I don't have to imagine; having browsed r/atheism in the past, I have seen this written by many of the people who post there.
In regards to r/atheism in particular, I think the place serves its purpose as somewhere for people in such situations to let out the bitterness and anger. From what I can tell, most people who post there are not long-term; they tend to move on once they've gotten it out of their system. I feel that hating it and ridiculing it is missing the point. I think it could probably do with not being a default subreddit though.