Sean, almost all of my reading says caffeine is good for you. The only situation I could think of that it might be bad is by using too much, but that goes with everything.
And, I have gotten use to being awake during my 8:00 classes and I like being ready to work the second I get to work, so I really suck ass if I don't have my morning coffee. That could be considered a slight negative effect.
Caffeine has been used for thousands of years with no ill effects, so I think it is as safe as water.