I beleive the problem is this.
The age of enlightenment took us from barbarism, to modern cultures.
However, the drastic change requried and still requires an ongoing compromise. The U.S constitution, had it been soley in the hands of certain founding fathers and didn't need broad appeal,
would have been I believe, a lot more unforgiving of religious nonsense. They had to, and still apparently have to, compromise on this, and let the peasants have their religious beliefs and happily deny reality, so that some form of society can be held together. We didn't really have a choice between "a purely reasonable form of government vs what we have", we had a choice between no government, or a compromise government (at least from that perspective we had no other choice).
Compromise always involves giving something up on both sides, and this is precisely the cause of what you see today in your OP. Maybe from here, we can now move forward to the next step that is closer still to purely reasoned, and maybe we'll then see another great leap forward in human prosperity and freedom (as we did with the intial adoptation of reason into our way of life).
The other thing that starts to surface more is th systematic application of reason to ethics. If it continues to be that we can identify reasonably, certain things as broadly ethical and unethical, eventually that means a clash between individual freedom, and ethics. Actualy this goes on non-stop as it is, but it will become a bigger issue the further that reason takes us. For instance, if it's demonstrably true (given XYZ) that guns lead to more crime/deaths, then it will always be a clash between the individual and the ethic and it's probably always going to be a compromise there as well.
In the end, unless humans change themselves physiologically (like gene maniupation), or chemically (like we all take drugs to make us less animalistic), we may not be able to overcome or basic animal brains to embrace reason more fully as a culture. We may need to create AI's who will have no such weakness and who will become our beneavolent benefactors, in that way, we may never become the perfect beings we strive to be, but we may be able to create them and they may rightfully pity us,and take care of us.
-Mach