If Atheists and rationalists focused on countering religion than God their argument will be heard more and even rationalized by people having faith.
There are a few problems.
First, faith and rationality do not go hand in hand
There are many fallacies and faults in all religions but whenever confronted the faithful will either try to change the subject, post irrelevant verses as the ultimate proof and if nothing finally bring it down the one basic tennant of religion which is faith.
Second, religion is basically the will and word of God and accepting that it has flaws in it, would nullify the whole concept of God being the All Knowing, All Seeing, Infallible etc etc.
Third, I have spent decades arguing with religious people and have come to accept the fact that convincing someone of the non existence of something or even questioning it is a fools errand as it is in the end all about faith. It is very hard to change the mind of someone who has accepted something to be 100% true without many objective reasons other that it being pummeled into them since birth.
There is a reason why believing followers of one true faith do not believe the followers of the other one true faiths.
There are many factors such as indoctrination, subjigation, education (actual non biased education, not just that someone is a doctor or an engineer), poverty, or even people who actually feel there is something far more superior in the universe and choose the option most suitable to them.
Religion is something that exists mainly because of misinformation and denying access to actual, unbiased information, but the brain should be in a position to assess this information which is very hard. I have been down that long road and it took me a long time to accept that what I was taught and knew wasn't the word of God due to the hundreds of logical fallacies.
My current stance is to let nature take its course, less and less of the newer generations are questioning religion due to the abundance of information and are moving away from it, I wouldnt have taken so long if I had Google in my teens, instead I had to research everything the hard way.
In conclusion, it is quite pointless to debate religion and to a certain degree politics with others who have opposing views as most people have already made up their minds and there is no point of trying to convince them otherwise.