1. It makes employees unhappy.
2. It gives abrasive customers an unfair advantage.
3. Some customers are bad for business.
4. It results in worse customer service.
5. Some customers are just plain wrong.
I think these reasons hit the nail right on the head (and he includes some fun examples).
(Via a comment at Behind the Counter, a blog that often includes examples of the Florida Wal-Mart where its author works getting ripped off by horrible customers.)
A variant of "the customer is always right" that also drives companies in the wrong direction for some of the same reasons is "the executives are always right."