Acknowledging their Pain
Regardless of whether or not you think the commenter was in the wrong, it’s important to say you’re sorry. An apology doesn’t mean you admit to any wrong doing on your part — it’s acknowledging your commenter’s negative experience and demonstrating that it you are sorry for their frustrations.
Your response should go beyond “I’m sorry” and directly mention what the commenter was upset about. You can say something like, “I’m sorry you had a bad experience with {xyz product}. In their {x number} years of business they have prided themselves in their friendliness and this doesn’t follow that standard,” will be more much effective.
This apology not only admits that you are sorry the product or business did not live up to full expectations, but flips the story to express the history of the product you are promoting and the level of service people should expect from them.
I try to 'agree before differing' (where possible) when responding to negative comments.
Also, sometimes its important to remember the motives behind the people arriving through Site Comments - they are not representative of my target audience usually.
It is often clear they have skim read the article and made broad assumptions to cut down on reading time and rack up another 'comment'.