That is probably true in most cases, but some of the exceptions are quite prominent, e.g., Coyne’s loud protest that it was questionable whether anyone who believed in the Resurrection (i.e., Francis Collins) ought to be appointed head of a scientific organization (the NIH), and the confession of one of the astronomers on the Iowa State tenure review panel for Guillermo Gonzalez that Gonzalez’s religious conclusions regarding fine-tuning did contribute to his vote against Gonzalez. When the public sees stuff like this, they may well conclude that what they see is just the tip of the iceberg, and that there is massive systemic discrimination going on – at least in areas of science concerned with origins. (I don’t suppose the public thinks that professors of analytical chemistry or meteorology discriminate against their Christian students, but it probably does suspect that cosmology and evolutionary biology professors sometimes discriminate against their Christian students.)
One thing that would help in this regard would be if scientists such as yourself publicly chided Coyne etc. when they show such anti-Christian, or more broadly, anti-religious prejudice. When prominent scientists appear to bash religious belief or religious scientists, the public is likely to take the silence of the majority of scientists as consent.
In the Gonzalez case a group of Christian scientists, the ASA, showed great concern that Iowa State might have discriminated against Gonzalez in the tenure decision, allowing factors (i.e., dislike of his religious beliefs) other than the normal academic standards to influence the outcome. Yet after reading scores of blogs and internet debate about the Gonzalez case, I have not read a statement by even one atheist scientist that the scientist who admitted voting against Gonzalez partly because of his religious views was acting improperly. (I don’t wish to re-try the Gonzalez case here and will not respond to anyone who wishes to justify his refused tenure. My point here is not that Gonzalez should have been granted tenure, but only that one of the reasons for the denial was not professionally ethical; his private religious conclusions from his astronomical studies should not have been held against him.)
So sure, I think most scientists are willing to live and let live when it comes to the religious beliefs of other scientists. But the public would feel more confident if on occasion a few atheist/agnostic scientists upbraided some of their more vocal atheist/agnostic peers when those peers seem to be indicating a hostility toward religious belief.