The threat of militant atheism is that they seek to marginalize Christianity (or Christians) in general and conservative Christianity (or Christians) in particular.
Atheists are not only a small minority with little power or influence, but they are also the most despised and distrusted minority in America. This makes them unlikely oppressors of Christians, a majority standing behind the levers of power in society, but this is what many Christians believe. They insist that there is a cabal of godless atheist secularists trying to marginalize Christians and Christianity. These feelings of alienation are genuine, but their target for blame is inaccurate.
Christianity (and by extension, Christians themselves) are suffering something of an identity crisis in America today. There was a time when conservative Christianity defined the basic boundaries, choices, and behaviors of people throughout America, including non-Christians, because it defined the assumptions and structure of most public institutions, public culture, and American politics. This is no longer the case, and Americans are increasingly able to just ignore Christianity.
Christians and Christianity are no longer explicitly and overtly privileged in culture, politics, or society generally. There is now greater attention being paid to other religions, other traditions, and other philosophies. American culture is now far more complex than it used to be and many Christians are frustrated because they feel alienated from what they think America should be. Many of these Christians grew up in an American culture which was simpler and more overtly Christian on every level. They were used to their traditions, their beliefs, and their people dominating throughout society.
This bothers many Christians because it represents a separation of their basic identities: at one time being an American and being Christian were combined, but today they are becoming increasingly separated. Christians want someone or something to blame for this and many have latched on to atheism, secularists, and godless liberals but they are wrong. Atheists are being blamed because they are among those who most obviously benefit from these developments, just as Jews were once blamed for all the ills of modernity and the Enlightenment because they so obviously benefited form liberalism, emancipation, and democracy.
Christians today remain a majority in America generally and in most communities. For many, this is viewed as a reason why their religion should continue to dominate. They believe that a majority should generally get whatever it wants and thus you'll often find them defend their position on various legal or cultural conflicts in that way: if most people in a community believe a certain thing, celebrate a certain day, or want the government to do something, then that's what should happen. The concept of "tolerance" is restricted: the majority only has to tolerate the minority insofar as they aren't eliminated, kicked out, or suppressed. The minority, however, has to tolerate the majority's exercise of legislative power to do as they will.
It's not marginalization when stores or communities broaden their terminology to talk about "holidays" at the end of the year rather than single out just Christmas for special promotion or endorsement. Even Christians celebrate more than one holiday during this time, so they aren't being excluded yet they complain about the failure to use greetings and words which do exclude others. In effect, some people's complaints about being marginalized are really complaints about how they are unable to continue marginalizing others.
It's also not margingalization when the government is prevented from promoting, supporting, or endorsing the beliefs, scriptures, or practices of Christians. The government is prevented from doing this with all religions, not just Christianity, so insisting on a strict separation of church and state simply means insisting that Christianity and Christians be treated like everyone else. Christians who complain about this are complaining about not being privileged over all others.
Thus what we have is the ironic situation in which some Christians are complaining about being marginalized because they are denied the social, political, or cultural power to marginalize everyone else. This is a power which Christian majorities used to have, but American society is far more inclusive and equal today, so this power has disappeared in many situations. It's not that Christians themselves are marginalized, but rather that they have been put on an equal level with everyone else. They are no longer privileged or told that they are better than everyone else. That's not marginalization, it's equalization, and it's definitely something which atheists fight for.