I think President Obama did the correct thing by not actively participating in the so called "National Day of Prayer", though probably for reasons different form his.  I'm sure the presidents reasons for not participating were primarily political while mine are religious.  
    The problem that many of us have with this event is it's lack of religious diversity.  It can't really be called "National Day of Prayer" when it's completely controlled by an Evangelical  Christian group that decides every year what the theme of the prayers will be and who can actively participate.  If you are Buddhist, Hindu, or even a Christian, but a member of one of the many Churches who's beliefs are significantly different from those of this organization, you will not be permitted to actively participate.  Of course, you can passively participate by sitting quietly and listening to them pray.
    If this is to really be a National Day of Prayer, the government needs to run it themselves, or at least have a large interfaith group run it.  At long as it continues to be run by an organization representing one church and one belief, it is not what it claims to be.