As usual, the truth lies somewhere in between.
Healthcare advocates do often caution against too much caffeine, and coffee in particular, especially for people managing stomach conditions like GERD and bone conditions like osteoporosis.
The other side of the coin
Before dismissing coffee entirely, remember that in addition to its troublesome acidic properties, it contains some antioxidant properties that make the pro/con question less straightforward.
For example, a recent animal study suggests that coffee may inhibit a protein associated with Alzheimer's. This study was conducted in mice, so only very limited conclusions may be drawn about this effect, but other health effects have been studied in humans:
Preliminary evidence in humans also suggests that coffee may lower risk of liver cancer, prostate cancer, and diabetes. And one study found no connection between coffee and life-threatening diseases.
Some controlled research has suggested that green coffee extracts taken as supplements or in food may support weight loss, although research in this area should be viewed with caution due to at least one study retracted because of methodological problems.
When used in moderation, coffee and other caffeine-containing products may safely help people who are trying to get fit find short-term motivation to get out the door.
The bottom line
Moderation is key, so people with healthy bones and stomachs would still be well advised to keep their limit down to 1 or 2 cups of coffee daily. Everyone is different, however, and in the end it's important to pay attention and notice how your body responds to caffeinated beverages.
Try not to rely on coffee as a substitute for sleep. And rely on good, nutrient-dense foods as a fuel source. Including 1 to 2 ounces of high-protein food with every meal keeps the body strong and blunts the rise in blood sugar after eating--meaning a steady flow of energy for you. Be sure to combine that protein with healthy fat (olive oil, avocado) and complex carbohydrates (whole grains).
Staying properly hydrated is also good for avoiding fatigue and supporting brain function and energy. So as part of a long-term health strategy, stick to your daily limit of coffee and experiment with other healthy drinks, such as water with a slice of lemon, or hot or iced tea.