Many computer users run a modified version of the GNU system every day, without realizing it. Through a peculiar turn of events, the version of GNU which is widely used today is often called "Linux", and many of its users are not aware that it is basically the GNU system, developed by the GNU Project.
There really is a Linux, and these people are using it, but it is just a part of the system they use. Linux is the kernel: the program in the system that allocates the machine's resources to the other programs that you run. The kernel is an essential part of an operating system, but useless by itself; it can only function in the context of a complete operating system. Linux is normally used in combination with the GNU operating system: the whole system is basically GNU with Linux added, or GNU/Linux. All the so-called "Linux" distributions are really distributions of GNU/Linux.
The point you might be overlooking is that the GNU userland was established back in the 80s. Most UNIXes (there were many, and at least a dozen "common" ones) shipped with AT&T or custom or (later) BSD versions of these userland tools.
GNU was brilliant because it was portable to most of those pathologically differentiated UNIXes, and it meant that arguments and behaviors were predictable, after you installed the GNU tools.
Then along came Linux. Of course it used the GNU tools. Everyone used GNU tools. The different part was that the kernel was free and not BSD (which had recently emerged from serious political and licensing drama, and -- if the old story is to be believed -- Linus was completely unaware of).
Soon there were dozens of operating systems sharing that kernel. The important categorization of them is that they were all Linux. And yeah, they ran the GNU userland, like every other non-pathological UNIX that wasn't BSD. Any other choice would have been hugely surprising (and doomed Linux).
So yes, GNU deserves prominence. But "GNU" wasn't omitted from the common naming due to any hostility or ignorance. It was just obvious, and not new or noteworthy in that sense.
It hurt RMS's feelings, and he has been vocal about it. Everyone agrees that GNU deserves much respect, but many people are turned off by the way RMS has reacted to his feelings of disappointment.
It's not fair, but few things in life are, and many people have difficulty sympathizing with RMS.
Interestingly enough, /g/ is obsessed with RMS and the regulars' attitude towards him is the epitome of a love-hate relationship. The sheer number of images they've produced featuring him is quite impressive.
So I really think that it is perfectly fine to name a system by it’s lowest possible encapsulated unit of software (kernel). In my case, this is Linux.
After all, he's going to go down in history first and foremost as the founder of the modern open source movement, that's not a technical thing per se.
Ouch, rms wouldn't be pleased with that statement ;) "we do not accept being mislabeled as open source supporters" -- rms
ADDED: To my knowledge, there are two areas where he's really, truly, significantly innovated: EMACS and GNU/FSF. The EMACS innovations are just not the stuff of serious history, however much we appreciate them while we're using it. GNU/FSF, that's big, and while (more than) minimal technical merit was required for it make a difference, the innovation was not technical per se (well, unless you look at the legal side, i.e. the GPL). Again, I'm trying to see how "history" will view him.
I myself use FOSS when I'm talking to an audience that knows it, but many if not most general historians are unlikely to make such fine distinctions, unless we get some really major object lesson in why his version of free software is really what we should be doing.
E.g. imagine a major spying on citizens, or more likely subjects, scandal from opening microphones by closed (enough) software. I know some land line phone system designers have deliberately made that impossible.
(I do, BTW, empathize with his cellphone attitude, I own one candybar "3rd world" cellphone that's almost always turned off unless I'm rendezvousing/coordinating with someone and/or it's an emergency. Mostly because of lifestyle and penny pinching, but I never forget that whenever I turn it on I'm saying "here I am!" to the towers it connects to, and on or officially off, it's almost never in a place where eavesdropping would be useful. And, hmmm, yep, when I'm out it's almost always with my father, and I take advantage of his always carrying and primarily using a cellphone.
Hmmm, come to think of it, there are a number of reasons we got along with each other, despite me being an unhidden arch-conservative type and he a rather liberal type, e.g. neither of us are very trusting of the powers that be.)
While his strict insistence on accurate semantics, such as GNU+Linux versus Linux and "free software" vs "open source," seems annoying, pushy, and generally weird, he has valid reasons to back the insistence up.
What reasons do you have to back your criticism of him up?