From the Journal of AMA: (JAMA, 26 Jan. 1994, p. 280-3.)
"There was a significant association between (drinking more) caffeinated coffee and decreasing bone mineral density at both the hip and the spine, independent of age, obesity, years since menopause, and the use of tobacco, estrogen, alcohol, thiazides, and calcium supplements [in women]."
"Bone density did not vary [...] in women who reported drinking at least one glass of milk per day during most of their adult lives."
That is, if you drink a glass of milk a day, there is no need to worry about the caffeine related loss of calcium.