The term "fundamentalist" came from theologically conservative Christian scholars who wrote a series of volumes defending the Christian faith titled "The Fundamentals."
A perusal of the volumes indicates that the use of "fundamentalist" as a derisive term has no connection to the reality of those books. They were written by real scholars with serious degrees from serious institutions.
Because the books were so widely distributed and enthusiastically received by many Christians, the word "fundamentalist" was coined to show identification with the message of the books. Over time, the word became an epitaph very much like the infamous "N-word" that contributes virtually nothing to understanding or discourse.
The abuse of the term has become even worse now that it is used to identify certain segments of Islamic extremism. More serious still has been the tendency of American progressives to cross-identify American theological conservatives with aggressive Muslim terrorists. Thus, we hear of "Texas Talibans" and the like. Such identifiers are particularly ridiculous considering the fact that an outsize proportion of our troops fighting Muslim terrorists likely identifies with the basic values of early American fundamentalism.
In response to the false (or provenance-challenged) Newsweek story about a Koran being flushed down the toilet, we have heard news of a riot among Muslims causing the deaths of several people. Such a response is unheard of in Christian circles and readily highlights the perils of cross-cultural religious comparisons. In other words, a fundamentalist is not a fundamentalist is not a fundamentalist.