It's important to differentiate between beliefs and reasoning. The problem isn't that people mistakenly assume that they are the same, but rather that people can assume that having 'good' or 'right' beliefs as ends in themselves, regardless of the reasoning process that produce them. I won't dismiss the value of having good rather than harmful beliefs, but relying on unsound reasoning processes doesn't leave much room for improvement and learning.
Human beings have evolved not only biologically, but also culturally. Perhaps one of the most important advances in our cultural evolution has been our ability to expand the definition of the 'in' group - the group we consider most deserving of kindness and assistance. Today most people's idea of 'us' is much broader than it was a few thousand years ago. How much further can the circle be increased?
It is true that early Russian Nihilism had a strong apolitical streak and that later nihilistic philosophies also tended to be apolitical in nature; nevertheless, even Russian Nihilism also contained a very strong element of political activism. Those who argued against the reality of traditional morality and authority also often argued that the social structures which served to uphold morality and authority should be taken down, by force if necessary.
Have you ever decided to come out as an atheist to your friends and family, only to have them react with anger or outright denial? Any atheist — not just former Jehovah's Witnesses — is likely to face this after they leave their faith. Many of us hope our associates will get used to the idea, but some never do. They may use guilt, angry condemnations, or other tactics to bring us back into their religion, all while insisting that it's for our benefit. This can be as hurtful as it is confusing.
It's not uncommon for atheists to argue that religion and theism are a sort of crutch that makes it easier for people to deal with problems in life, so perhaps it's not a surprise that some might try to turn this around and argue that atheism is actually the crutch. How, though, can mere disbelief in gods act like a crutch in any manner - no matter how metaphorical? The problem lies in misrepresenting atheism as if it were a belief system.
Have you ever had a Christian suggest to you that you try out believing in God and Jesus, 'just in case'? Have you ever had a Christian suggest that you pray to Jesus or cry out to God, just to see if you would get a response? Curiously, Christians offering such advice don't seem to be very keen on following it themselves, at least when it comes to 'trying out' other religions.
Many traditional bigotries have centered around obvious physical characteristics: race, ethnicity, gender, etc. Because of this, some claim that there can't be any serious bigotry against atheists because an atheist isn't defined by any obvious physical characteristics. You can't pick an atheist out of a crowd and you don't even know someone is an atheist unless they say so. That, however, is part of the problem for atheists: their invisibility helps perpetuate myths and suspicion about them.
Sometimes the rhetoric heard from American conservatives, especially religious conservatives, almost sounds more like a medical report than a political analysis: America suffers from 'decay' and is 'sick' because of the 'corruption' and 'infection' of liberal, subversive elements. In order for America to be 'healed' and once again start down the road to greatness, the infection has to be removed
Not all churches and religious organizations have been content to live within the rules. Quite a few have attempted to evade the rules, either secretly or very openly, in order to allow churches and religious groups to participate actively in political campaigns even while retaining their charitable tax-exempt status.
Barack Obama's real opinions about secularism are either confused or simply unknown — he has expressed both sentiments which can be construed as pro-secularist and sentiments which can be construed as anti-secularist. These contradictions might charitably be interpreted as typical political posturing: telling everyone what they want to hear in order to avoid offending anyone. On the other hand, maybe he himself is sincerely confused due to conflicting impulses.