The difference is in the "Rise of the Atheists" phrase. That shifted the emphasis toward an 'increase' in atheism, which the article doesn't seem to bear out:
Among the reasons for the change a spike in the number of American adults who say they have no religion. The Pew study, released Tuesday, found that about 20 percent of Americans say they have no religious affiliation, an increase from 15 percent in the last five years.
Scholars have long debated whether people who say they no longer belong to a religious group should be considered secular. While the category as defined by Pew researchers includes atheists, it also encompasses majorities of people who say they believe in God, and a notable minority who pray daily or consider themselves "spiritual" but not "religious." Still, Pew found overall that most of the unaffiliated aren't actively seeking another religious home, indicating that their ties with organized religion are permanently broken.
The first link was the one posted in the Religion forum, which has become predominantly atheist. To me, the data in this article would seem to indicate that more American citizens, especially the young, are seekers, whether they use that term or not.
It would be interesting to see some additional polling aimed at that unaffiliated group to see how they break down into various Deist, theistic agnostic, atheist, minority religion, etc.