HQ's are an easy place to overload on points. They have such extensive wargear lists, its easy to pop on 5 point upgrades, or otherwise "just in case" wargear. Consider, say
Captain - 175
"Makes him a pretty dastardly character"
or does it? If you instead look at a Librarian, for a lot less, you get a boost to your whole army, depending on the powers. (I'm looking at you null zone) It's certainly less 'killy', and in toe to toe, my money is on the captain. But then consider that with the points saved, that the libby could buy a plasback to ride around in (well, hijack one)and that null zone plus 3 ap2 shots makes for a dead character real quick. This goes double for taking multiple HQ's. Say you decide to toss in Cassius (admittedly a steal) at 125 points. Does he really do more for your army than a rifleman? Do you need to tack a ~200 point character into a CC squad? What are you charging that needs (Or is worth) throwing another couple hundred points at?
It's all about efficiency. By spending less on your characters, you have more points to go around the rest of your army. Which brings me back to the title, HQ Tax. Consider your mandatory HQ slot as a 100 point 'tax' on your army, and build the rest of it from there. I can't imagine an army that can't get a par HQ choice for around 100-130 points, at least for those unfortunate enough to not get 100 point psykers with hoods and 2 powers.
Later this week I'll post my thoughts about overall army efficiency, and tomorrow (with luck) I'll have my full collection dusted off for a photo shoot.