Everything in moderation...
I think anything can be "bad for you" in large doses, but I think just like everything else in life, coffee is fine in moderation. I too have read studies on how coffee is harmful to drink, and how coffee is excellent to drink. But I've actually read more good about it than bad.
It just goes along with everything else. Carrots are good for you, but if you eat too many you turn orange. Lean Chicken breast is good too, but if that's all you eat, then you could get a build up of protein in your urine. You hear studies about how red wine is good and how drinking alcohol is bad, but I think all these things can be beneficial to the body so long as they are not overdone or overdosed on.
Coffee has many benefits such as antioxidants and can help you get a better workout when you are low on energy, and I think 1-2 cups a day is totally doable and beneficial. Just listen to your body and you'll know when too much is too much.