The Right Way
The illogical words, the inappropriate deeds of some people, and the superstitions which have entered into religion, have no relationship to Islam, and they ought not to be considered a part of it. One should not accept them. Instead, one must fight against them. Rejecting such things, is by no means for disbelief in the true religion. You must only stick with the truths of the religion and get rid of all the fallacies.
Although I do not have the wisdom to tell you what to do, but allow me to say: when you find any fault with me, please try to explain it to me in a manner that I have the capacity to understand. If I ask you a question about the reasons why some act of worship is done in the way it is, or if I question the philosophy behind some others, do not get upset with me, and do not call me a disbelieving Kafir.
In School, I have studied mathematics and natural sciences and have become mostly familiar with physical reasoning. But some religious matters seem unacceptable and complex to my mind. I have to ask about such matters. If you explain the answers to me in any easy to understand language and in a nice and logical manner, I will be convinced and will accept them. It would make me happy to feel that I have been able to find the solutions. And probably, this will help me solve other problems too. Therefore, you should be pleased with this line of my questioning, since I am doing this only to search for and to find the truth.