When I ask people what they believe and why, the "why" is the important part. The "what" is far less important. If you are not willing to address the "why," then you are not being intellectually honest with yourself... -Matt Dillahunty, The Atheist Experience Ep. 813
When I discuss deep philosophical issues with people, I always start by saying that I am a skeptic first, a philosopher second, and an atheist third. I stand convicted that some that openly converse with me believe that I am a radical talking head or maybe even the Devil himself. But, I must say, my intentions are noble: the truth is what I seek.
My skepticism arose as a priceless faculty. At my former college, things were taught on the basis of tradition and oftentimes included an emotional tinge. Although, once I started to get serious about objectivity, once I actually cared about my beliefs, I noticed that my preconceptions were unjustified. Skepticism molded me into the thinker I am today. It is a skill that requires patience - which it seems, humorously, that I retain only in the realm of ideas. From this skeptical standpoint, I will discuss the differences between religious and secular morals.
Religious morals are conceived and extrapolated from texts that are supposedly divine. The texts usually give a (supposedly) divine commandment with the explicit claim that the commandment is from God himself. (It is interesting to note the justification for why the religious believe this: the commandments are correct and moral because God said them. Why did God say them? Because he is God. How do you know he is God? Because it says so in the Bible/Quran/Upanishads/etc...). But this point brings up many conflicts. The first is famously recorded in Plato's Euthyphro dilemma. The second rests upon the authorship problem: How do we know if A) God truly commanded the moral commands or B) if it is solely the human medium's opinions? And the third issue is a general problem with religious claims: How do you know that the command is correct/absolute? Of course, this question inevitably ends with something along the lines of "You must have faith." No, I must not have faith. Faith is weakness and a scapegoat.
On the other side of the morality debate lies secularism. Secular morals are, first and foremost, obtained through practical reason. I concede that an accurate goal of human morality is to maintain a standard of well-being. (It could be argued that morals do not rest upon such goals, but I do not wish to address this here). When one thinks of well-being, one could say that such a state includes human flourishing or the absence of pain/harm. This is why many secular thinkers rely so heavily upon John Stuart Mill's harm principle. Also, the claim that morality should be linked to a sense of well-being is supported by scientific evidence. There are many studies that show the negative effects of all sorts of different harms (psychological, sexual, physical, emotional, etc.). This seems to be apparent knowledge. By using practical reason, erroneous claims about morality are eliminated. Moral relativism, for instance, holds no ground where practical reason is utilized. Just because some cultures practice female genital mutilation does not make that action morally correct. In secular morals, moral guidelines are determined insofar as it is supported by the use of practical reason.
In light of this delineation between the two modes of morals, I must admit that morals obtained through religious means are deleterious and causes the corruption of human thinking. This is the type of thing that "justifies" a Muslim extremist to follow the Quran's commands to commit the murders of the infidels. It is also the type of thing that causes a Christian to bomb abortion clinics or fight against marriage equality because it is condemned in the book of Leviticus and others. I am personally convinced that mindful Christians are fighting moral conviction when they openly condemn gay marriage; there is no way they can reasonably justify these claims.
Such is the poison of morals derived from holy texts.