This is not to say that the DM should never do it, just that it is the tool in the toolbox that is in the box, but rarely gets used. A DM that uses it every session (or even worse, every encounter) needs to spend more time thinking about his encounters, and balancing them.
Thinking about the times I have seen this worst in play, an issue that creeps up is when the DM becomes too willing to modify off the cuff. This results in encounters changing wildly from too easy (then the DM overtweaks) to overpowering (then the DM overtweaks again) back to too easy. This situation breaks suspension of disbelief and ruins the feel of the encounter.
I think our difference of opinion on the matter comes from how we have used / seen the tool used. When it is used with great diligence, it can have positive results on the gaming session. When it is not used with diligence, it ruins the gaming session.