The argument against rules derived from religious belief is that, because the adherents of a religion believe that the rules are Divine, they cannot change; whereas rules that are acknowledged to be man-made can change to meet the changing circumstances and attitudes of society.
This opinion, again, demonstrates how Atheists perceive religion the same way religious extremists do, and not the way most adherents of religion view their faiths. It is an opinion that could only be formed by someone outside the mainstream of a religious community. Anyone who belongs to a religious faith, and who interacts with other members of that faith, will realise that there is constant, ongoing, robust debate, discussion, and variant interpretations regarding religious rulings, and how faith-based values should be manifest in social relations. To be ignorant of this fact, one would have to be an outsider to the religious community either because they lack of religious belief, or because they hold radical religious beliefs that isolate them from the rest of the community.
Muslims understand that most of Islamic jurisprudence is man-made; it is comprised of rulings extracted by scholars from the scriptures through a rational interpretive process which considers the time, place, and circumstances where the rulings will be applied. This is called Fiqh, it is continuously evolving, and no one treats it as infallible.
Shari’ah, on the other hand, is regarded as Divine, and therefore fixed and unchanging. This is what the Atheists are talking about. But what they do not know is that the Shari’ah contains extremely few explicit rules; most of which pertain to matters of worship. When it comes to issues like the penal code in Islam, this is almost entirely derived from Fiqh and has such a flexibility and scope for differing interpretations and mitigating conditions that it would make secular laws look rigid by comparison.
Indeed, the truth is that religious communities (certainly Muslims) are far more willing to adapt and change than many of those who accuse them of absolutism.
But here it must be pointed out that we do not always disagree with secularists and Liberals out of blind adherence to unquestioned religious laws, but out of sincere, rational, moral convictions. It is self-serving and lazy to dismiss our objections as the result of our backwardness and inflexible religious beliefs, rather than actually listening to our reasons and being as willing to question their own beliefs as they are to condemn ours. Perhaps we need to reform, or perhaps they need to reconsider. But while we are generally open to the possibility of reform, secularists and Liberals are seldom willing to admit that their ideas may be flawed.