I haven't looked at the study.
However, the graph presented by no means entails that Protestants are becoming atheists more than Catholics are. In fact, it could be that Catholics are significantly more likely to turn atheist than Protestants are.
Suppose Catholics have many more children than Protestants. If those Catholic children are more likely to eventualy become atheists than Protestants are, it could produce a graph such as the one shown--a flat line for Catholicism (which experiences strong positive and negative changes, from the kids and deconversions), and a rising line for atheism.
As for Protestantism, even if the decrease is explained totally by flights to atheism, the magnitude of Catholic apostasy could just outstrip that of Protestant apostasy. As long as Catholic fertility matches Catholic apostasy, the graph will not change.
A new study by the Pew Forum on Religion and Public Life [executive summary; full report; New York Times cover story] found that 19.6% of adult Americans answered a question about their current religion by saying they were atheist, agnostic or “nothing in particular.” In 2007, the figure was 15.3%; in 1972, it was about 7%.
Some relevant quotes from the executive summary: