Very interesting read, both the OP link and this thread lol
I agree with many of the things in the OP with in reason.
First off the word hate. I think thats the wrong word, hate is strong and though just my personal experience ive never encountered anybody that hates "religion" in real life. Ive encounter a couple nutball extremists that hated Islam and Muslims but again those people were clear nutballs.
as for me ive never had an issue with religion or people because of their religion. My church and religion are just fine by me. Its individuals that have issues.
But where many comments and parts of the OP have nailed it is the huge hypocrisy, bigotry and some flat out evilness you find among INDIVIDUALS that claim to be practicing religion, use it as a tool of force and or a shield for there gross behavior.
It's important to remember those people are still individuals and not representative of the religion.
If these extremist were outed more by their religion/church the results were be better but unfortunately many times they are not and the opposite happens. They are protected and also covered for. And please focus on that second part because its whats important. Nobody is REQUIRED nor NEEDS to out somebody based on their religion, race, gender, political stances etc etc matching. You dont need to show your disapproval for some racist, or child molester, or terrorist, or fake priest simply because you share something with them like religion but if you participate in the cover up or excuse train thats an issue. Sadly IMO this happens to often in religion.
So to summarize issue 1 are the hypocrites, bigots and flat out evil INDIVIDUALS among religions people. These people should never be covered for and on the other side people have to realize they are just individuals.
Next are the extremist that want to force their religious views on others whether its strict religious rules or their very subjective views of that religion and again these INDIVIDUALS do not represent the religion but they are wide spread and unfortunately many are in positions of power and or influence. This issue needs treated the same way, these individuals should never be covered for nor should excuses be made for their great disdain for rights, freedoms laws and out constitution.
So issue 2 is easy, religion is not the rule of law in america thank god and it never will be. So you best to leave that part of your religion at home. As soon as you try to stop others from having the same rights as you do or others from having the same freedoms and you site your religion you are part of the problem. But again you would be an INDIVIDUAL .. not a religion.
If people in general would mind their own business (when no rights, law and freedoms are being infringed on or broken), not try to force their views on others and realize this issue is an individual problem I believe that much of any distaste for "religion" (though its misguided because its not a religion thing) would subside greatly.