First off, I agree partially with your point about "flip-flopping." However, the obvious answer to your question is not that people are suspicious of politicians change their ideological positions upon logical reflection alone, but rather those who seem to change their position to conform to popular/party opinion.
Also, it should be known that there are segments of the population other than right-wing extremists who are less than enthusiastic about the results of the enlightenment; specifically, branches of academia. Though I realize no such individual is running for office, but the larger concern I have is that those with religious convictions are being broadly categorized as anti-science lunatics, and those who are atheist/agnostic are regarded as levelheaded rationalists (as you have done). The point is, there ARE rational Christians, and there ARE anti-science intellectuals, even if these people are most probably the exception and not the rule. In the end I think it's most useful, intellectually honest and generally right to make judgments on a case by case basis.