Is caffeine bad for you if combined with good nutrition and sleep habits?

No: The literature on caffeine is tremendous and if it was actually causing problems beyond headaches (if you reduce your dose) and sleeplessness (if you overdo), we'd have found it. There is a mild withdrawal syndrome but since no one has trouble quitting, it seems stupid to call this an "addiction". Folks who work long hours may need caffeine; i know no doctor-in-training who did not use it.

Probably ok: Caffeine doesn't seem to have detrimental long term effects (in doses under about 400mg/day), but for some people can cause anxiety, mild dependence, and other unpleasant symptoms; it can be dangerous for people with underlying conditions such as cardiac arrhythmias.