The problem is that reddit is trying to be both a neutral platform and a cohesive community at the same time. No one gets mad at phpBB when someone deploys a forum with an objectionable theme because it's understood that they had no involvement, they just provided the code for anyone and everyone to use in accordance with a FOSS license. reddit tried to do that with hosted subreddits, but it also tried to cross-pollinate and make one big reddit family and see everyone on reddit.com as "redditors". That results in a lot of infighting and resentment (/r/the_donald v. /r/enoughtrumpspam, /r/atheism v. /r/christianity, etc.), not to mention some doxxing, harassment, brigading, and invasions.
It's tense in the real world when people with diametrically opposed worldviews are forced to mingle, but it can sometimes go OK because the human aspect tempers it. Occasionally, with especially open-minded participants, a friendship can be kindled. That doesn't seem to happen at all when these people are not put in a room together, but on a message board, especially an anonymous message board.
reddit didn't know whether it wanted to be a warm fuzzy community, for which common ideals and values are foundational, or whether it wanted to be an agnostic, neutral, unfeeling platform provider. IMO that's responsible for a big part of the culture clash that we see on reddit, and it's left them in the awkward position discussed here.