It's a different issue. Acidification of the oceans happens mainly due to dissolved CO2 [0], while the acid in the atmosphere is mainly due to SO2 and NOx.

Greenhouse gases were not discussed in the article and were not part of that study, but as you may know, they're still going up. [1][2][3] (Oh yay, the sum of CFCs is actually going down.)

[0] https://en.wikipedia.org/wiki/Ocean_acidification

[1] http://www.esrl.noaa.gov/gmd/ccgg/trends/ (This page is so scary.)

[2] http://www.esrl.noaa.gov/gmd/ccgg/trends_ch4/

[3] http://www.esrl.noaa.gov/gmd/aggi/aggi.fig2.png // http://www.esrl.noaa.gov/gmd/ccgg/aggi.html