Some religious doctrines require humans to obey an authority above the pursuit of rational thought. These religions are therefore based on faith not reason. When humans give up reason, the only method left for decision making is faith. Sometimes, faith may not match your immediate needs. If you take a contrary position against the religious elites, brute force could be used against you.
Presumably, these doctrines declare to their faithful followers, that the rational thought process has already been done and therefore, there is nothing to be concerned about.
Some states have also maintained a link between religious practice and the law. This has the potential to cause conflict when individuals are not religious or are from a minority group.
An example is the Spanish Inquisition which was established in 1478 by Catholic Monarchs. It was setup to maintain Catholic orthodoxy in the kingdoms by identifying as heretics, those who refused to convert from Judaism and Islam to Catholicism. Many other groups were caught up in this persecution and the churches use of "brute force". It was eventually abolished in 1834 (356 years later), during the reign of Isabella II.
Most religions provide good principles by which to live, but it's done in a contradictory way whereby they suffer the conflict between Individualism and Altruism. Finding a balance between the two requires careful consideration of the impacts on both personal freedom and collective welfare.
Probably the most important principles in Christianity and Judaism, are the "Ten Commandments" which are:
1.You shall have no other god but me
2.You shall not make any idols to worship
3.You shall not take the Lord's name in vain
4.Remember the Sabbath day and keep it holy
5.Honour your father and your mother
6.You shall not kill
7.You shall not commit adultery
8.You shall not steal
9.You shall not bear false witness
10.You shall not covet your neighbours goods
Buddhism, Hinduism and Taoism are examples of religions without a deity and therefore allow humans to use reason by which to live.
Confucianism consists of 'Three Fundamental Bonds' and 'Five Constant Virtues'. Three fundamental bonds are between husband and wife, father and son (mother and daughter), lord and retainer (employer & employee). The five virtues are: benevolence, righteousness, propriety, wisdom and trustworthiness.
The Hebrew mantra from the Book of Exodus 21:23-27 - English translation "An eye for an eye". This is the principle of reciprocal justice measure for measure. This religious mantra is one way to minimize the death toll of the innocent in case of an outbreak of war.
Living based on 'Gods Will' could sometimes contradict an individual's moral code, and when it does, an important decision needs to be made. Your health and happiness are at stake.
Probably the most important contribution to humanity is the concept of ethical reciprocity, which has appeared in many forms within many cultures and religions throughout history.
This principle appears in Christianity as the Golden Rule and is expressed in the Bible:
Matthew 7:12 - So in everything, do to others what you would have them do to you, for this sums up the Law and the Prophets.
Luke 6:31 - Do to others as you would have them do to you.
It also appears in Judaism in the Talmud:
Shabbat 31a: - What is hateful to you, do not do to your fellow: this is the whole Torah; the rest is the explanation, go and learn.
and in Islam in the Hadith:
Sahih Muslim: - None of you truly believes until he wishes for his brother what he wishes for himself.
and in Confucianism:
The Analects 15:23: - Do not impose on others what you do not wish for yourself.
and in Buddhism in the Udanavarga:
Udanavarga 5:18: Hurt not others in ways that you yourself would find hurtful.
and in Hinduism:
Mahabharata 5:1517: - This is the sum of duty: do not do to others what would cause pain if done to you.
and in Taoism:
Tao Te Ching, Chapter 49: - To those who are good, I am good; to those who are not good, I am also good; thus all attain goodness. To those who are sincere, I am sincere; to those who are not sincere, I am also sincere; thus all attain sincerity.