I'm really appalled at how many people here are having knee-jerk reactions and taking the show the wrong way. This is not supposed to be anti-Bush or anti-American or anti-WoT. I have never read or heard anything from Ronald D. Moore or David Eick that implied any kind of political slant coming from them (I have met them both a couple of times now). I've always seen the Cylons as a group of religious fanatics who are trying to convert their enemies by force - sounds more like Islamofascists to me.
The fact that the humans are polytheistic while the Cylons are monotheistic is meant to show that the humans have a culture of diversity and differentiation not unlike that in America. And the Cylons can only focus on one thing, which is their fundamental and violent beliefs.
Also, when it came to the election last season, I found it very, very clear that Laura Roslin represented conservative ideals while Gaius Baltar was more in line with the secular progressives. And wouldn't you know it: Gaius won (eventually), and let the Cylons march in and take over. Just like what would happen if a "secular progressive" got elected here.
I think that some people who was complaining really never watched the show from the begining.. You are right and that is how I saw the show from the begining...