I haven't seen the film, or seen much else of what Maher has to say on religion, but I feel like it is a complex subject of which he makes too little. He doesn't talk about the historical advantages of religion, only the disadvantages, and does not say what system of thought would fill the role of religion were it forgotten. As he said in the interview, he is only asking questions, but these questions are banalities; they are stock phrases of free-thinking agnostics who are uninterested in researching the issues that will be left gaping open without the support of religion.
For one, he mentions how religion comes at a high price, citing the religious wars of nonsecular times. But what he does not mention are the benefits of the alliance of Church and State that were of great value before the close of the 18th century. Pre-industrial Europe may have been worse off without the Church. The main benefit of this alliance was that it made the European people into good political subjects, a task which was not easy in pre-industrial times, when peasant uprisings and rebellion were the main concern of kings. The acknowledgment of these benefits and acceptance of such an alliance is evident in the ideas of Locke and Priestley, which served as an impetus for the revolution of liberalism and democracy in both Europe and America. There is a reason why "In God We Trust" is our national motto; religion was necessary for the granting of civil and political liberty.
In my mind, the ideology that replaced religion at the close of the 18th century was Nationalism. This was made possible by the Industrial Revolution, which made people aware of the advantages in living under a strong central government. It was of course also influenced by the American Revolution, the French Revolution, Locke, Priestley, etc., but I think that the Industrial Revolution was the ingredient that made the shift in ideology first possible. Nationalism answered the question of "How can we make good political subjects out of the people?" which required attention before any other ideology should be accepted. People were motivated to become good political subjects out of self-interest like that non-iniquitous kind introduced by Smith; this self-interest being a result of the Industrial Revolution.
But it has been over two centuries since 1776 and 1789, over 60 years since WWII, and Nationalism is slowly fading, especially after our indulgence in unnecessary and disastrous wars like those of Vietnam and Iraq. We have already landed a man on the moon; we have already become the world's superpower. What ideology then would make the American people into good political subjects? The Christian religion has evolved over time to meet the incumbent political need; this is seen in Henry VIII's usurpation of the Catholic Church, and his establishment of the Anglican Church, which allowed himself more power over matters as simple as divorce. It is seen in the Puritan movement as a response to corruption in the Church of England. But the Christian religion has not had the chance to evolve since Nationalism took precedent; it is not out of the question to consider that maybe another major reformation in the Church could fulfill the need to make better political subjects of the American people. This is certainly an issue we are facing today.
Bill Maher's political ideology seems to be the exercise of reason in relation to national interest, but as I said, Nationalism is fading, and it is not an argument or ideology that would convince the American people as a whole. This is especially true in this corporate world where self-interest has usurped national interest, where the two are no longer the same. It seems the new ideology will be a corporate ideology, which appears to be at odds with the reason, Nationalism, and self-interest of the middle class, those very same motivations by which Maher votes Obama.