I wonder if the next challenge for them is the strong representation from r/atheism on their frontdoor? I say that as a very irreligious person who guesses that discovering their new selves is exciting for (I imagine, predominantly) American youth. But some pretty bland ra-ra makes it through and I can see that being off-putting for religious types and "this again?!" for those for whom a lack of belief is the default rather than something new and outrageous within their community.
Yes, I know people can create an account to customise their experience, but some fair percentage of their traffic is going to come from people not interested in taking their involvement to that level.
Doubtful. These are deep-seated patterns that have been playing out in online communities for decades, and every "oh we'll just build a new thing that won't have that problem" attempt has... had the same problems.
For examples, and some interesting thoughts on the issue, start here:
1. Allow any user to add themselves into the community; and then,
2. allow the course of discussion to be set by majority rule.
The site (or subreddit, or newsgroup, or whatever)'s focus and usefulness will gradually disintegrate as people in secondary demographics join (e.g. for programming, people interested in web design) and then tertiary demographics join who are only interested in things the secondary demographics like, and actually don't care about the original, primary focus of the community at all.
For examples of tertiary-demographic takeover, see Reddit's /r/music and /r/movies. The primary demographic wanted media discussion; the secondary demographic wanted to discuss specific pieces of media; and the tertiary demographic just wanted links to new media they hadn't heard of. (Which—for /r/music at least—when combined with the average new-Internet-user's set of "music they've heard of", the way people have a more positive association with music they've heard before, and the way democratic interest floats up the most agreeable items, the front page becomes basically "Reddit's Top-40 chart.")
Any community that avoids this will fundamentally have to avoid doing either #1 or #2.
Seriously, folks, read Clay Shirky. The man knows what he's talking about.