Militant atheist is often used as an implied anti-atheism put-down. Although it is arguably an accurate description in certain cases for a particular interpretation of the word "militant", that word also carries with it a number of other associations which are definitely not true. "Militant atheist" is therefore a troll phrase, as it is almost always used to covertly insinuate falsely-based criticism.
- vigorously active and aggressive, especially in support of a cause: e.g. "militant reformers"
- engaged in warfare; fighting
The first definition is arguably applicable to the most active or assertive defenders of atheism, although "aggressive" carries with it a further implication of physical aggression -- which is definitely not the case for any but a few isolated atheists.
The second definition, however, does not apply to any known atheists -- at least, not in the sense of being engaged in warfare (other than verbal) about atheism. (There are certainly many atheists involved in warfare -- as soldiers or freedom fighters, for example -- who might therefore literally be described as "militant atheists", but there are no known instances of the phrase being used in this sense.)
In short, then, the primary definition carries with it some negative connotations that are untrue, and these connotations are further reinforced by the second definition (which is completely inapplicable).