What we do say is that it’s hopelessly misleading to go around saying “Science and religion are compatible.” It would be more true to say that science tends to undermine all or most traditional forms of religion, making them less plausible, putting pressure on the religious to thin out their supernaturalist, providentialist views of the world, and so on. The result is that much in the way of actual religion really is threatened by the advance of science. Claiming otherwise is, we say, likely to be disingenuous (or, to be fair, simply mistaken).
We then have a great deal to say about the various ways in which science does this. In particular, we tend to criticise ideas such as NOMA, which seem to us to be full of problems. For example, NOMA gives a characterisation of religion that is totally untrue to the historical experience of the phenomenon.
None of this is about acting in ways that are uncivil.
The idea that in-your-face mockery is an inherent and inevitable part of Gnu Atheism comes, pure and simple, from accommodationists who—desperately avoiding arguments about substance—concentrate on tone. It’s all about framing, and it’s been somewhat successful.
An alarm bell should go off when you see fellow atheists chastising us for being “dicks.” As often as not, those very critics behave in exactly the way they deplore. That, after all, is the lesson of the Tom Johnson affair.