I challenge the initial framing of there being a choice to be made between "explicitly atheist" and "respectful to theists." One can, in fact, choose to be both at once.
But, yes, I would agree that not everyone makes that choice.
This isn't unique to atheists, incidentally... many explicitly theist communities choose not to be respectful to other theists, in much the same way.
In any event, I would agree that if there are people around who consider respecting their fellow group members an actively bad thing if those group members aren't thinking correctly enough, then at some point I've got to make a choice about what I value more.
This post grew out of a very long discussion with the New York Less Wrong meetup group. The question was, should a group dedicated to rationality be explicitly atheist? Or should it make an effort to be respectful to theists in order to make them feel welcome and spread rationality farther? We argued for a long time. The pro-atheism camp said that, given that religion is so overwhelmingly wrong on the merits, we shouldn't allow it any special pleading -- it's just as wrong as any other wrong belief, and we'd lose our value as a rationalist group if we began to put status above truth. The anti-atheism group said that, while that may be true, it's going to doom us to be a group exclusively for eccentric nerds, and we need to develop broad appeal, even if that's hard and requires us to leave our comfort zone.
Things got abstract very fast; my take was that we need to get back to practicalities. Different attitudes to religion have different effects on different types of people; we need to optimize for desired effects and accept what tradeoffs we must. We can't appeal equally to everyone. So I came up with a sort of typology.
The Four New Members
Annie