I don't know exactly where you would set the bounds of "militant atheism" but it's clearly the case that many people we might classify as such are not Marxists. None of the most famous "new atheists" (e.g. Dennett, Harris, Hitchens, etc.) are Marxists, as far as I know. It seems like the mistake you are making is in thinking that if two groups of people share a common goal then they must either entirely share the same beliefs or that one group must be a dupe of the other. But that doesn't follow at all. To make an analogy, there are libertarian posters on this board with whom I share some views, for example opposition to excessive state power, or the war on drugs, or trends towards elements of a police state. But in other areas my views diverge sharply from theirs, e.g. progressive taxation and social policy. That fact that we have some overlapping aims and views does not make either of us dupes of the other.
Similarly, Marxists and "militant atheists" share an antipathy towards religion and some common goals about reducing the power of religious institutions. Some also share a belief in materialism, although the dialectical materialism of Marxism is sometimes a bit idiosyncratic. But otherwise members of these two groups often have very few other political views in common. Someone like Dennett is not attempting to foment a proletarian revolution.