Strictly speaking, I think a fundamentalist is someone who starkly observes and adheres to the fundamental tenets, teachings, and commandments (for more dogmatic belief systems) of their religion. However, the term seems to be commonly used to refer to people who hold beliefs or opinions perceived by the person using the term as exclusivist, intolerant, or hostile toward other beliefs and/or people who hold them.
Using the first definition, I believe a "fundamentalist atheist" is nonexistent by definition: atheism, the lack of belief in a deity or deities, isn't a set of teachings or a religion that has any "fundamental" aspects except said lack of belief.
If one uses the second definition, then I think the line becomes more blurry: it seems to me that, while there's truth to the statement that there are many intolerant and narrow-minded atheists (as there are intolerant and narrow-minded people in every group, be it religious or not), the relative unpopularity of the atheistic stance compared to theistic one--albeit tending to vary from place to place--gets atheists more readily branded as "fundamentalists" in the sense of the second definition than theists.
As an example, I have yet to hear any atheist claim that even a single theist will suffer for any amount of time in another realm or life because of their theological stance, but I frequently hear the opposite. Furthermore, if the former claim were made, I have little doubt that it would upset and possibly shock more people than the latter would--again, because more people are used to the former claim, and also because of the aforementioned unpopularity of atheism relative to theism (and even more so when compared to certain categories of theism than others).
For something I'd consider enough to label an atheist intolerant, bigoted, etc., (basically applying to them the second definition of "fundamentalist" I mentioned), an example would be saying that all religious people are intolerant, or accusing them of being anti-scientific due to their being religious. Talking about all religious people as if they were a homogenous group that shared the same views on everything strikes me as bigoted, although it can also be a result of ignorance (or both bigotry and ignorance).
Generally, I think the yardstick most people use for measuring what constitutes militant or "fundamentalist" atheism is stricter than its counterpart against which theistic claims are measured. The more a statement or claim is made, the more people get used to accepting it... and the converse is also true, hence the contrast between the strictness of the two yardsticks, in my opinion.