We have concepts like humanism which reject external authorities and rely on the individual to make a choice as to what is fictitious and what is the truth. Similarly, Luther's reformation movement placed emphasis on personal interpretations rather than following the orthodox stance. Now this can lead to problems but for the most part I have to assume it has been a great revelation.
Most if not all would agree that there are passages from the sacred texts of the Abrahamic religions that in current modes of thinking are outdated, barbaric and immoral. For instance, the people practicing idolatry probably did not think they were living a life of sin, without morals, as they were stoned to death in punishment for their beliefs. Thankfully, that idea for punishment went out the window long ago, though it is still practiced by some Islamic cultures.
The enlightenment not only has allowed us to question which morals are worthy and what is just, but also relieved the constraints on science. Perhaps this is where theology and science are most at odds. Through the advocacy for reason, the movement has given us a glut of advancements. Physics, biology, chemistry, all flourished. Democracy was revived from the ancient civilizations as the idea that there exists a contractual arrangment between society and the citizen took off. This ultimately gave rise to the Liberalism movement as well.
Without covering all of the enlightenment, a monumental task itself, I'll jump ahead to current times and events. There are many subjects today which pit the modern enlightenment ideals against one of it's founding theories, divine right. Divine right was the idea that a reasonable God made the Universe, gave it order, and through Him and his earthly representatives we have proof of His power. This seems to have met in a stalemate as some Western nations have began to stagnate. The idea that perhaps we have gone to far. How can that be though?
We haven't embraced all of our citizens, to pull those up who can't pull themselves up. Rights are still denied by what seems to be some archaic baby blankee clutching. The social contract is perverted to where we have individuals hoarding wealth, while our fellow man and woman struggle. While there are those who advocate for these people, their message might be discarded by yet another perversion, media and democracy. The polemic discourse between entrenched combatants, who clutch at straws and jump at every opportunity to discredit those on the other side of the aisle, is the most infuriating of all.
While the social contract has been perverted, the rights we give up to the government for some measure of social order, the governing system itself has been perverted to a state of help your friends, political gains, very much not in the civilians best interests. That is furthered by a media that refuses to report objectively, so that we must wade through the muck to find some hint of truth.
Modern morals as advanced as they are, seems to me to have plateaued. A modern enlightenment or some such school of thought is needed, or perhaps just a re-evaluation of what it is we are doing and where it is we came from. I'd like to think we're not beyond our reason.