And to dllthomas' point, the controversy is the 'it'. Naming things is a pain, and naming computer things is a bigger pain. That was the root of the controversy.
Today most people who use a Linux distribution on their machine will say they run Linux or "distroname" (like Ubuntu or CentOS) on their machine. They don't say they run Gnome 2/Linux Kernel 3.x/gcc 4/gnu utils 2.8. By RMS' reasoning (and he is very precise in this) the "Operating System" is not "Linux" it is "GNU/Linux". They even added a field for it in uname(1) (-o).
The "Operating System" is a combination of the kernel, the editors, and user tools, and the compilers. Go back and read his original announcement, this is his definition:
"To begin with, GNU will be a kernel plus all the utilities needed to write and run C programs: editor, shell, C compiler, linker, assembler, and a few other things. After this we will add a text formatter, a YACC, an Empire game, a spreadsheet, and hundreds of other things. We hope to supply, eventually, everything useful that normally comes with a Unix system, and anything else useful, including on-line and hardcopy documentation."
By that original definition, we shouldn't even bother calling it GNU/Linux should we? Its just GNU. I expect taking that position though would be quite unpopular.
As the Wikipedia page alludes to, there were at least two camps at the time. Many, like myself who 'grew up' on the UNIX side of the house, the Naming Hierarchy was 'kernel->[userland]->window system' So it was SunOS->SunTools or SunOS->X/News. If you called something a "UNIX" system it meant that the kernel was based on the design architecture of Thompon, Ritchey, et al from Bell Labs. SunOS, IRIX, SystemV, and Unicos were all "UNIX" systems even though their userland code and window systems (if they had one) varied. Even in RMS' original statement of purpose, the first component of GNU was a kernel, and some other bits.
So to someone with the same background as I've had you could call it Linux/GNU (hierarchy preserved) or "Ubuntu" based on Linux with GNU tools. But Linux as the kernel architecture is at the top of the naming chain, not GNU.
For folks who came up from the DOS/PC side of things the 'window system' was the primary naming tool (in this case Windows). It was PC-DOS/Windows for a while but Microsoft decided to go all out and make "Windows" the brand/trademark they hung their hat on, and we got Windows/DOS, Windows/NT, Windows 98, Windows XP, Windows Vista, Etc.
As dllthomas illustrates, the interpretation of the 'it' part rooted the disagreement, and which side of the disagreement one resonated with seemed strongly correlated with ones early exposure to naming conventions.
My belief is that the emotion in the discussion came from egos, or people feeling person A or person B's contributions or impact were over or under valued. We can see some of that in the comments here where people emotionally jump to a conclusion that I'm down on RMS (I'm not), or even partisan in this debate (I'm not that either). There is ample documentation that Linus' goal with Linux was to write a new OS from scratch kind of like (but better than :-) MINIX. And there is ample documentation that RMS' goal was to create an operating environment that was unencumbered by onerous restrictions. It was fortuitous the Linus' work was so successful, and it was fortuitous that Linus could leverage the work done in the preceding 9 years in making tools available for him to use.
But it was also clear that Linus wasn't specifically supporting the GNU project by writing Linux (although he subscribed to the philosophy). When RMS started claiming as part of the project it set up this little tempest. Perhaps the term 'annex' is too emotionally charged to be used for that action.