The answer to this is, as always, basic education in Islam. Underlying the statement is one big assumption that happens to be wrong — that the core teachings of all religions are the same. When you clear up this misconception, the argument "fundamentalism is fundamentalism" will lose its foundation.
The truth is, not all religions are the same. Islam has several precepts in its core teachings, written in their most holy book, the Qur'an (which you have hopefully read cover to cover by now) that are different from any other religion.
For example, it says in the Qur'an it is a Muslim's duty to refuse to be friends with a non-Muslim, to deceive them if it will help the cause of Islam, to strive to subjugate non-Muslims politically, and if they resist, to make war on the unbelievers and slaughter them. It doesn't imply this. It doesn't require any interpretation or reading between the lines. It says this quite clearly. So a "fundamentalist" who is following Islam will be (and, as you can see around the world, IS) quite a bit more willing to kill people just because they are not Muslims than, say, a fundamentalist Buddhist or Hindu. Read a fairly complete comparison between Islam and Christianity here.
Another thing very different about Islam is that it is written in very straightforward prose by a single man. Most non-Muslims don't even know this much about Islam. The Qur'an isn't a collection of writings from many different sources. It isn't metaphorical. It isn't strewn with allegories open to interpretation.
If you have read the Qur'an, you may speak with authority about this. The person who says "fundamentalism is fundamentalism" is either a Muslim giving you taqiyya or a (probably well-meaning) non-Muslim who has never read the Qur'an. Your best approach is probably to convince them that they cannot know what's true about Islam until they, too, read the Qur'an for themselves.
That's how I've approached answering this objection before, and it has worked fairly well. If you have tried a different approach, we'd love to hear it. Please leave it in comments on this article.
Read more: Are All Fundamentalists Dangerous?