I think that when one calls someone a fundamentalist in the pejorative sense in which it is used on this board, one is accusing that person in part of being biased against people outside whatever group they happen to be a member of. Being closed to other ways of thinking is part of a fundamentalist. Fundamentalists see other modes of thought as wicked, mendacious, or at the least wrong on every important question. In my mind, prejudice is a hallmark of fundamentalism.
I think we've learned from past discussions in this forum that the definition of "atheist fundamentalism" is pretty mushy, so maybe those who accuse atheists of being fundamentalists here are not trying to imply prejudice in their accusations. Furthermore, I implied a distinction in my earlier post, so I will provide some examples in which bigotry and prejudice specifically are alleged.
In a thread last spring, I was accused of making a post that was "blatantly anti-Christian." The post was almost completely off-topic but didn't refer to Christians as stupid or ignorant. All it did was express skepticism and fail to speak about Christian ideas in reverent terms. The only value judgment applied in excerpt I quoted is the word "fanciful."
http://www.democraticunderground.com/discuss/duboard.php?az=view_all&address=214x166820A thread about President Obama's appointment of Dr. Francis Collins to head the NIH spurred a subthread dealing with anti-religious bigotry. A poster expressed his/her disagreement with Obama's choice (without explaining why) and was accused of "anti-Christian bigotry."
http://www.democraticunderground.com/discuss/duboard.php?az=show_mesg&forum=132&topic_id=8562062&mesg_id=8562130A post in the same thread accuses "some here on DU" of being biased against anyone who is religious. This post does not use the term "bigot," but in substance it is an accusation of overwhelming bias against the religious.
http://www.democraticunderground.com/discuss/duboard.php?az=show_mesg&forum=132&topic_id=8562062&mesg_id=8562120In another thread about Collins, a poster was accused of "simple-minded bigotry" for calling Taoism goofy and saying that religion and science are incompatible because religion is completely false.
http://www.democraticunderground.com/discuss/duboard.php?az=view_all&address=132x8521668#8524137Here is a thread by a DUer complaining of being called an anti-religious bigot. The post was in response to discussion in another thread which I am unable to locate, so I cannot evaluate whether the OP's previous statements were justified or not. I trust that the discussion in this thread is somewhat illuminating, however. The issue was then-Sen. Obama's association with anti-gay evangelist Donnie McClurkin during the primaries.
http://www.democraticunderground.com/discuss/duboard.php?az=view_all&address=132x3634353#3634473