This judge's ruling seems to be based on a very narrow definition of the establishment clause:
A federal judge on Thursday struck down the federal statute that established the National Day of Prayer, ruling that it violates the constitutional ban on government-backed religion.
"[I]ts sole purpose is to encourage all citizens to engage in prayer, an inherently religious exercise that serves no secular function," a Wisconsin judge wrote in the ruling, referring to the 1952 law that created the National Day of Prayer.
"In this instance, the government has taken sides on a matter that must be left to individual conscience," wrote the judge, Barbara B. Crabb.
Yes, praying is "an inherently religious exercise," but that just means it's common to most religions. The voluntary day isn't an attempt to "establish" one religion above all others, which is what the Constitution's drafters were concerned about. They didn't require government to be hostile to the very idea of religion, which seems to be where a lot of modern interpretation, including Judge Crabb's, seems to have landed. The law purposely requires the day to be one other than Sunday, so it isn't even inherently Christian.
The government setting aside one day on which I can pray, if I feel like it, doesn't seem very coercive to me. The director of Americans United for Separation of Church and State says the decision is a "tremendous victory for religious liberty," which seems more than a tad hyperbolic.