Thank you for writing. I can see a sincerity in your words and I thank you for that. I am also impressed by your admission that what is done by some in the name of Islam is wrong. You might be surprised how many times I have had Muslims refuse to admit that some of the cruelties done in the name of Islam are wrong. You stand out in the crowd by this statement.
I freely admit and teach that much that has been done in the name of Christianity in the last 1500 years has been degrading to the cause of Christ and has been done in direct disobedience to the teaching of scripture. In fact, many who call themselves Christians are not. You become a Christian by following Christ--not by calling yourself a Christian. There is a real distinction between what people claim and what they are.
Now, despite this agreement, there are a couple of things you mentioned that we would disagree on, but I will mention them (as you say) in peace.
First, I find that Muslims have trouble understanding the American concept of separation of church and state. Unless I misunderstood you, you seem to do so as well. In Islam, the religion and the state tend to be one. In America, there is freedom of religion (though we continue to fight for this freedom). Any one religion is not to control the government, and the government is not to control religion. You mention the atomic bomb dropped in Japan. I will not discuss the choice to do this, since it was a political decision. But it was not dropped on Japan in the name of Christ as an act of our religion. It was an act of war by our government. Whether right or wrong, it was not done by extremely religious Christians who were praising their God for the glories of being allowed to destroy the enemy in such horrific terms. This is definitely a distinction that Muslims need to address.
Second, as I read the Quran (and I am reading it), I find many teachings that encourage the actions of the violent Muslim extremists. In other words, it seems to me that they are the ones that are following the plain teachings of the Quran and that Muslims like you are like liberal Christians who do not believe the clear teachings of the Bible. Basically, that is the purpose of the articles we have on Islam that seem to be so offensive. Perhaps an interesting discussion would be found in addressing these passages and hearing how Muslims like you explain them. This would be of great interest to me. It seems that the extremists just take them for what they say.
Finally, let me add this. I know that there are Muslims who would make good neighbors and that most Muslims are not a personal threat to my life because I am a Christian. You certainly seem to fit in that category. I also do not think that Muslims are by nature any more evil that any other group of people--including Christians. In fact, the Bible teaches us that all men are wicked sinners by nature. That includes me as well as you. There must be a payment for that sin in order to appease the wrath of God against wickedness. The Bible teaches that this payment was made by Jesus Christ when He suffered our judgment of sin on the cross. However, this forgiveness cannot be applied to us individually until we look to Him as our Saviour and trust in Him for our eternal forgiveness of sins.
I know you will disagree with what I have just said, and that is alright. However, I encourage you to find out about Jesus Christ. Read the gospels--especially the Gospel of John. See who Jesus is and what He did for you. Think on what it would mean to have your sins totally forgiven in the person of Jesus Christ. What a blessed thing it is to have your sins forgiven and to have Christ in you as the hope of glory. That is the gift God has given to me. It is also the gift He offers to you.