It appears that the researchers might have expected an increased risk of stroke among coffee drinkers, but the surprise finding was that it can be protective against stroke. As long as the women in the study were non-smokers, and drank 2-4 cups a day long term, there was a reduction in the incidence of stroke. Other caffeinated drinks (tea, soda) did not have the same effect. Decaf DID show the same effect. So it's probably something other than the caffeine causing the protective effect.

Other recent studies have shown that that coffee may not increase the risk for coronary heart disease and may be protective against type 2 diabetes. Data on stroke up to now has been conflicting.

this study
--analyzed data from the Nurses' Health Study
--n=83,076 women, free of stroke, CAD, diabetes, or cancer at baseline
--coffee consumption assessed in 1980 and then every 2 to 4 years thereafter
--24 years of followup ending in 2004
--over this period, 2280 strokes occurred among the women: 1224 ischemic strokes, 426 hemorrhagic strokes, and 630 strokes of undetermined cause
--adjusted data for: age, smoking, BMI, physical activity, alcohol intake, menopausal status, hormone therapy, aspirin use, and diet
--evidence for a protective effect for intakes of 2 or more cups per day vs less than 1 cup per month
--after adjusting further for high blood pressure, hypercholesterolemia, and type 2 diabetes, the inverse association remained significant
--the association was stronger among never or past smokers than among current smokers

SOURCES
http://www.medscape.com/viewarticle/588403?src=mp&spon=17&uac=89474MT
http://www.ncbi.nlm.nih.gov/pubmed/19221216?dopt=Abstract