Because in the letter of the law they are right and if they complain Apple will be obliged to yank it. A precedent has been set with another piece of GPL software.
And the person making a fuss about this knows it will likely create outcry on the web/blogs/gadget sites (and the majority won't derstand the subtleties and complexities of software licensees and the GPL). This will damage Apple's PR and further enforce the idea the Apple are over zealous and controlling.
And no one wins. There is another thread where others have contributed their views and it is explained in further detail.
Like I wrote in that other thread, my interpretation differs from yours:
"Apple manages to keep VLC out of the app store, VLC being one of the [few free] media players on there that will play a wide variety of content from sources other than Apple. Yet Apple will still be seen as the good guy in the end, since they at least did approve the app and in the end, by finally pulling it from the store, only did what was legally required of them. Honi soit qui mal y pense."
If you assume, that Apple would rather not have VLC on the app store, then they actually now got someone to do the "dirty work" for them. But yeah, maybe I'm underestimating the negative effect on Apple's PR (and/or overestimating their dislike of apps like VLC) ...