Question: My internal model of academia is that (1) as a group we are one of the most tolerant of biological and philosophical differences (e.g., gender, sexual orientation, and religion) and (2) that we are likely to take extreme views on issues related to our research. I have no evidence for either of these and they seem potentially at odds in that it seems strange that people would be so passionate about their research and be blase about their religion (or any other philosophy). Is there any work that characterizes the level of tolerance of academics on various issues?

Answer: 
There is [a recent study](http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2063742) which generated quite a bit of noise and seems to indicate that racial and gender biases do indeed exist in academia (at least in the U.S.). The researchers sent e-mails to professors pretending to be a prospective graduate student, and response rates varied widely depending on the ethnic- and gender- markers in the purported student's name.
I think it might depend on the field. For example, if you are in a Biology department, you're likely to be labeled as "ignorant", "dumb", or "coward" if you are Christian (or Jewish, or Muslim or any religion that believes in a God who creates), regardless of whether you believe in evolution or not, and regardless of what your actual religious beliefs are. Generally, in natural sciences that's a pretty common trend I think. One could argue that this is more related to the second point you mentioned, rather than the first one, but given that this intolerance, as I said, is regardless of the opinion of the religious person about the origin of life and rules of physics, one could also argue that having this opinion that "any religious person is incapable of appreciating science" as an assumption, is a form of intolerance. 

(There is a documentary about Christian professors in science (or biology) departments who were not tolerated by their colleagues and were discriminated against, but I couldn't find it now)

When it comes to ethnic and racial tolerance, in my experience, a level of racism and orientalism that would face condemnation in the US (but not necessarily in Europe) is not uncommon in academic communities in Europe. That being said, my impression is that they're still considerably more tolerant than an average person (or at least an average conservative) in that society. 

But overall, I perceive academics to be more tolerant than the median member of the society.