I received this article on the STARFLEET News Service feed this morning.
Although I agree with the general idea of what the author is trying to say, I feel it necessary to clarify his description of Star Trek as "atheist".
First of all, I don't know if Gene Roddenberry (The Great Bird of the Galaxy himself) was actually an atheist. I'm not aware of any statement he made either confirming or denying this. Although I don't think it's unlikely. He was a communist, of sorts, and therefore of a considerably secular bent. Atheism, secularism and communism are often found together.
That being said, it should also be noted that although The Great Bird did invent Star Trek, and retained considerable creative control over the first two seasons of the Original Series, the first six feature films and the first few seasons of The Next Generation, he was actually involved in creating less than half the sum total of all Star Trek. And even then, he wasn't responsible for every creative decision made under his command. Roddenberry was, by all accounts, a team player who took a lot of input from the experts he surrounded himself with.
Taking all of that into account, it's probably quite a fair comment to suggest that overall, Star Trek has a pretty atheistic (or at least non-theistic) message. Despite several references in the Original Series to the "real God" or the "one God", presumably put in place in order to appease the conservative Christians of the day, most of the characters are atheists or agnostics.
In every case when we encounter a god or gods in Star Trek, the being in question turns out to be just another life-form, or in some cases a sophisticated computer. One episode, Who Watches the Watchers, even deals with Captain Picard becoming the object of a newly formed religion amongst a community of primitive aliens.
Some of the characters in Star Trek are religious despite the knowledge that the objects of their adoration are not divine.
Most notably are the highly religious Bajorans whose gods, The Prophets, turn out to be a community of non-linear, non-corporeal aliens living inside a nearby wormhole. Despite this discovery, the Bajorans continue to practice their religion, praying to and worshipping these life-forms who are only peripherally aware of their existence.
Commander Chakotay, a Native American descendent, practices his religious rituals in full knowledge of the science behind his trance-like states and hallucinations. This doesn't seem to stop him.
I don't think it's fair, however, to claim that Captain Kirk killed God. This statement is obviously referring to Star Trek V: The Final Frontier. In this film, a crazed Vulcan hijacks the Enterprise and takes its crew on a trip to the centre of the galaxy, where he believes is the place that creation began. Although the rest of the crew and passengers appear convinced, and even Kirk goes along with the whole thing, it's never clearly stated that the place is Eden, and the being encountered there is God.
Rather, I feel that the conversation between Kirk and the "God" entity confirms that the being in question is yet another alien life-form, who only pretends to be God. We've seen at least one other character like this in Star Trek: the alien Ardra posed as an evil deity in the TNG episode Devil's Due. Also the manifestation in which the being presents itself (as a large, glowing, translucent head) is also shown in another episode, also close to the "centre of the galaxy". Although it's never stated explicitly, I think it's quite obvious that the "God" Kirk killed was a rogue Cytherian who contacted Sybok by means of a mind-altering probe.
The Star Trek universe is thick with god-like beings (Q, Douwds, Metrons, Organians, Olympians, Prophets, Pah Wraiths, Sporocystians and so on), none of whom are actually the God of Earth's monotheistic faiths.
It could be argued that Star Trek just never examines that god, or that Star Trek maintains he doesn't exist. Either way, I don't think there is enough concrete evidence in Star Trek canon to be able to make a conclusive call in either direction.