While I greatly respect Hitchens and would avoid any argument with him, he is wrong on the National Day of Prayer.
With his “You can be proud of this great tradition of intolerance” statement, Hitchens falls victim to projection. He projects his own argument's weakness on others. This is something the left is frequently guilty of.
The National day of Prayer is not an establishment of any religion and therefor does not fall under the purview of the First Amendment. Secondly it is voluntary and no one is compelled to participate.
This seems to be 100% inclusive to me. Any religion can participate as no one religion is preeminent and those individuals who do not wish to take part do not have to do so.
It is Christopher Hitchens who is practicing what he call "the tradition of intolerance" through his exclusion of religion.