Everyone is automatically subscribed to them, and a large part of redditors are very young, ie., immature (though there are exceptions). The recent changes to r/atheism improved it a lot, and I think removing it from the default will improve it even more, as it will get rid of a lot of griefers and trolls. The level of discussion went up. Not that there is anything wrong with having tons of memes like the old one did, it should just be another sub-forum though.
R/atheism is great at completely puncturing the protective bubble religion lives in, and it shocks the holy hell out of a lot of religious people, who basically think it's full of bigots because they can't handle it, but it also can get people to start questioning some basic assumptions of religion through biting sarcasm and satire.
A lot of the criticism in the old r/atheism could be juvenile because of the age of subscribers, though on point nonetheless. Many subscribers were brand new to atheism, as a lot of the younger generation is, and are pretty pissed because of the religious environment they were raised in was terribly harmful, so it's a great place for them to vent.
This is a good move overall. Now that sub forum is still a resource for new young atheists while not drawing every oversensitive person who are shocked, SHOCKED, people could be so MEAN as to make fun of an idea,and a really bad and harmful one at that.
Same reason r/politics got taken down. Too liberal, too mean to conservatives, etc. etc. Atheists need a place to vent, especially young new ones. And there are more atheist forums popping up all the time! All trends point to religion diminishing in the US in public life and overall, and I'm very happy about that 
Edit history
= new reply since forum marked as read
