Aren't atheists hurting their cause and the cause of science or evolution by mixing in arguments about atheism, theism, and religion?
A popular complaint about some atheists, one that is raised not just by religious theists but also by secularists and other atheists, is that atheists allow their atheism to intrude into other arguments. For example, it is alleged that atheists improperly mix up promoting science and attacking anti-scientific ideology with promoting atheism and attacking religion. Doing so, it is argued, offends religious believers who would otherwise be willing to help to fight anti-scientific ideologies.
Superficially, at least, there may appear to be some validity to this argument — or at least to the concern which this argument expresses. From a political perspective, it's wise to acquire as many allies as possible in order to better ensure success and therefore avoid driving away potential allies by attacking unnecessary or irrelevant targets. At the same time, though, it's not wise to misidentify the nature of the problem or opposition that one faces.
This is why atheists aren't necessarily making a mistake when they combine advocacy for atheism with advocacy for science, or attacks on anti-science ideologies with attacks on religion. Although it's true that there is no inherent and necessary connection between the two, in practice the anti-science ideologies that are typically being tackled are based on religious beliefs. It's impossible to effectively deal with those ideologies and defend science without addressing the root causes for why people adopt those ideologies and attack science.
The debate between evolution and creationism is the primary context for this criticism of atheists, and it's also a perfect example of why the criticism is misguided. Creationism only exists because of religion — whatever form it takes, it is nothing more than a religious ideology designed to undermine modern science for the purpose of preserving and promoting traditional religious beliefs about morality, politics, and social power structures. It's impossible to even define or discuss creationism without also discussing religion — and Christianity in particular — so it shouldn't be a surprise that one cannot criticize creationism without also criticizing religion.
Attacking anti-science ideologies like creationism is thus not a "separate battle" from criticism of religion, religious beliefs, and religion's place in modern society. It's certainly possible for an atheist to make an irrelevant criticism of religion when trying to defend science or attack creationism, and it would be legitimate to complain about that, but there is no basis for saying that two issues are unconnected and should never be combined. On the contrary, in a nation where Christian leaders claim that the absence of indoctrination into their religion and the presence of biology classes cause incidents like the massacres at Columbine and Virginia Tech, it would be irresponsible for defenders of biology not to question what Christianity really provides after all.
At the same time, though, it's been common for critiques of creationism to focus almost exclusively on science and the facts, never really mentioning the religious aspects. This is what critics of atheists want to see because, they say, including religion in the critiques will drive away religious believers whose feelings will be hurt when they see attacks on their religion. It's not at all clear, though, that this tactic has done much good — America remains more opposed to evolution than any other industrialized nation. There doesn't appear to be any evidence that constructing arguments on the basis of what won't make people feel bad is effective.
Sometimes the accusation that atheists are making a mistake by mixing their atheism with their defense of science is based on the argument that atheists are trying to say that evolution proves the nonexistence of God, or something similar. To the extent that any atheists claim that any one aspect of modern science definitively disproves the possible existence of any sort of god, criticism is legitimate — but it is rare to find any atheists making such an argument.
It's more likely to find atheists arguing that multiple lines of evidence from multiple scientific fields demonstrate that God, as traditionally conceived of, is unlikely at best and perhaps impossible. This sort of argument is not susceptible to the aforementioned criticism, and any gods not disproven through such arguments are unlikely to matter.
At the same time, people making this accusation against atheists don't seem to have a problem with theists who make analogous arguments. Atheists who criticize theistic evolutionists are attacked for pushing away possible allies, for example, but the same theists who write books and articles arguing that evolution supports their brand of theism are not held to the same standards. Why is it wrong for atheists to argue that evolution supports atheism, but OK for theists to argue that evolution supports their theism? Why are atheists pushing away possible allies for criticizing those theistic arguments, but theists aren't pushing away allies for essentially arguing that atheism is wrong?
It's a double standard that can best be explained as based on anti-atheist sentiment — why else are atheists chastised for behaviors and attitudes that are ignored when expressed by theists? There is value in not insulting believers' feelings for no reason, but it's not legitimate to subordinate concern with the truth to concern for their feelings. If telling the truth makes a person feel bad, that's something they must learn to work through for themselves, not demand that others stop telling the truth. It's also not enough to say that criticism of religion is, in theory, not necessary for defending science — critics must demonstrate that a particular attack on religion is not necessary for a particular defense of science.