That would depend on what part of Roddenberry's life you're referring to.Gene Roddenberry was an atheist.
When he was a young man during the Second World War he was a Southern Baptist.
On August 6, 1969, Majel Barrett married Gene Roddenberry in Japan, in a traditional Buddhist-Shinto ceremony. At that time, Roddenberry in multiple interviews professed to being a Buddhist. There no indication that Roddenberry was an atheist during the creation, or production run of TOS.
According to Susan Sackett , who was Gene Roddenberry's personal executive assistant for seventeen years, during the late seventies Roddenberry believed in "The All" the universe's creative force, or God.. (Inside Trek: My Secret Life with Star Trek Creator Gene Roddenberry)
In the novelization of ST: TMP Roddenberry made this Spock's religion. Vulcans have the ability to perceive a oneness with The All
Roddenberry's belief in atheism would appear to have been during the last years of his life.
There are positive Christian - monotheist themed episodes during TOS. None of them were written by Roddenberry as the principal writer though.He went out of his way to have anti-religious themes in his stories.
Of the small number of stories primarily written by Roddenberry which do you feel possessed a "anti-religious theme?"
