For some people with GERD, coffee is very bad for them. My wife switched from coffee to tea for this reason. Tea is pretty fabulous for her, and I gather there's at least some documented health benefits on that front as well.
Edit: GERD = http://en.wikipedia.org/wiki/Gastroesophageal_reflux_disease
Second Edit: To be clear: I agree with the parent article, I think coffee is close to harmless for MOST people, and very well might have some positives.