Let's start getting into details because we both have fair points.
I'm not asserting all subjective beliefs are harmful or negative. But some beliefs have to have credence and reflect objective reality. For example, Kim Davis and Christianity's assertion that homosexuality is a sin. This is destructive in nature and harmful to the homosexual community. It creates discrimination and segregation. Other beliefs like swine being unkosher is questionable but harmless to society. I could care less what people eat as long as its not other people. Some vegans would argue here but then I digress. We have to draw a line against specific types of beliefs that are harmful to society and cannot be proven. It doesn't matter if those beliefs are religious in nature either. I find that reasonable, do you?
No, I don't. I don't regard beliefs as either inherently good or bad; such a concept seems, itself, to be largely derived from Christian doctrine (heck, about 70% of the US's values are rooted specifically in puritan morality, which I've observed being a large behavioral influence even in staunch atheists; consider H.P. Lovecraft). Beliefs are what they are, but they can't be regarded as having inherent qualities of "good" or "bad", since they don't exist in a vacuum.
Kim Davis' belief is harmful because it exists within a context that both enables and encourages her to act that belief out in a way that's harmful to individuals and our cultures. The same, however, could easily be said of beliefs that our culture would regard as virtuous; consider the well-known declaration that "all men are created equal". When taken out of context, it enables the erasure of things like from-birth disabilities, inherent physical differences, etc., and by extension encourages this idea that "everyone has the capability to do everything, and thus anyone who asserts that they can't do a thing is just being lazy". In the context of the original document, this isn't the case; for one, "men" refers specifically to white males over 21 who owned property, and for another, the equality is only in reference to the idea that everyone that "men" encompasses has equal and inalienable right to "life, liberty, and the pursuit of happiness." However, cherry-picking seems to be a valued tradition in the US, at this point, such that we now have the painfully inaccurate, and in many contexts quite harmful, notion that "America is a free country".
Or, closer to the topic, even the assertion that religious ideas are not to be regarded as sacrosanct and thus free to be mocked, could potentially enable cultural discrimination and segregation
because many US cultures are so deeply religious. The assertion is something I fully believe, even as a religious person. But also as a religious person, I can't ignore its possible long-term negative implications or consequences.
Scientific experimentation is about reducing uncontrollable variables, such that the experiment is performed in a figurative (sometimes literal) vacuum. While certainly a great thing, I wonder if this has created a mindset in certain people within the scientific community, that things should only be looked at independent of everything around them, even outside the laboratory setting. That couldn't be a more inappropriate way of looking at the real world outside the lab; EVERYTHING exists within the context of everything else: the Butterfly Effect.