The Mormons and the Seventh Day Adventists have sponsored a great deal of research to show that caffeine is bad for you. The bias was doctrinal (neither group uses caffeine because their understanding of their founders instructions was to avoid caffeine (coffee AND tea), though "Mormon tea" contains ephedra. The studies were often "justified" by the observation that coffee was addictive, caused jitters and heart palpitations in the extremely wired, and headaches for those enduring withdrawal. The puritanical reasoning was that "it's a drug (and the drinkers really enjoy it), therefore it MUST be bad for you."
The rebuttal research was often funded by coffee industry money and by folks who really wanted their morning coffee (or tea). But their initial views were often more or less summarized as, "caffeine isn't 'that' addictive, so it really isn't a strong drug, and its more harmless than alcohol." They were largely hoping for a "mostly harmless" finding. So, the discovery that there really did appear to be benefits to coffee and tea were actually a surprise to both groups. You will note that the wikipedia entry is considerably more negative in the initial paragraphs, but then is described as mostly harmless - even pregnant women can consume up to two cups a day of a drug that is labeled as both a teratogen and a mutagen. So, clearly the debate goes on.
The irony is that while the evidence that caffeine is harmful to individuals is mostly absent, socially it has been considered a threat for several centuries. It has been outlawed far more often than any other drug until the drug wars of the last century.