I've heard both sides of this story, and I just don't buy the 'audiophile' explanation that says if you don't like the sound, you need to change your setup (instead of resorting to the tone controls).
In my opinion, that's pretty much an impossibility since every recording I play through my system is quite different......some sound perfect to my ears with no tone controls used, but there are others that appear to be 'missing something', and so a little tweaking with the bass, treble, or midrange can work wonders in bringing a subpar recording to life. I don't believe the need to tweak certain recordings arises from weaknesses in my system - those recordings would sound imperfect to me no matter how fantastic the setup.
Granted, if your idea of the perfect system is for the sound output to be as true to the original recording as possible, then yes, using tone controls to alter the sound is an abomination. Like all of us here, I want the sound coming out of my speakers to sound great, but I don't have anything against using my tone controls to make my music sound the way I want it to, even if it isn't absolutely true to the recording.
The way I see it, audio is all about making the listening experience enjoyable to you. If using the tone controls makes that experience all the better, why not use it?