I think I have offered such evidence in my post previously, just by citing the same plot as you did:
Of course they’re legally free to speak out whatever they want. But even if our speech is legally protected, we should still be careful about how and what we speak, because some kinds of speech may have a real impact on other people beyond the simple meaning of the words. For example, many of the egregious behaviors cited in your OP are protected by freedom of speech. Repeatedly quizzing a fellow board member about their religious beliefs, pronouncing them atheists, insulting reporters, being ignorant - none of these things are illegal, even if they are unethical. So, I’m not at all saying that atheists should “remain silent” about their beliefs or their past. But being in a position of power on campus and making strong statements which effectively communicate “anybody who seriously believes in religion X must be stupid” may intimidate a student who identifies with religion X, whether the professor intends it or not. I just think everyone, whether they’re religious, atheist, or otherwise, should be sensitive about the effects of their words.
There are not many overt racial bigots in academia, yet we still do care about unconscious racial bias affecting the environment we create for underrepresented racial minorities in academia. (And I think such a concern is eminently justifiable, because implicit bias is real, even among people who normally don’t think of themselves as “racist”.) In the same way, even if few professors are outright like Dawkins, how many harbor an implicit bias against religious students? I don’t know for sure. It’s likely that this issue of anti-religious bias in academia is understudied, compared to bias against other underrepresented groups in academia. At least one study has already found a degree of unconscious bias against students who identify as evangelical: "Are scientists biased against Christians?" - from the Brownell and Barnes group. To be clear, I don’t think it’s as serious of a problem as racial discrimination, given that someone’s race is usually far more apparent than their religion in everyday interactions.
But what does an atheist professor in a liberal coastal area like Massachusetts have to fear from Christian judges and politicians who hold power in places like Alabama and Mississippi? (Now, of course there are also atheists living in Alabama and Mississippi, so I would not disagree with your point regarding those.)
I’m not going to even try to answer your points about culture, geography, diversity, history, because as someone trained primarily in science I don’t have the knowledge or expertise about American history, culture, and society to perform an intellectually responsible and informed analysis.
It seems that you are conflating between moral justification and practical realities. You also insinuate that I don’t care about improving the quality of life in the US, which is not what I was trying to say.