A friend and fellow author that I have a great deal of respect and admiration for is having a crisis of confidence. I will not name him but I too have suffered from this type of criticism. Some people can not tell a plot element from an endorsement.
When a murder occurs in a story, is the author endorsing murder?
When drug use happens in a story, is the author glorifying it?
As authors, I believe that the interesting stories are told on the edge. Somewhere on the border of normalcy and madness there is a place where drama comes from. That place can be mundane or high brow. It can be common or rare. It is about people in conflict facing adversity and without it our stories are just so much soggy granola.
I have read stories that glorify drug use. I know what they are when I see 'em. Yawn. I have read stories that are nothing more than a common masturbation fantasy typed with one hand. Snore. You know what they have in common? They are simply not interesting.
Touchy subjects can be addressed if the author handles it right. If you start reading a story and stop four chapters in because a character smokes a joint, then you don't know what happens in the other umpteen chapters. You miss the character suffering negative consequences like failed relationships and hanging out with a lower class of people. You miss him getting busted and asking himself what's wrong with me. You miss out on that characters chance at redemption or his fall into jails, institutions or death.
So you see something about a story that makes you uncomfortable. GET OVER IT.
Here's YOUR chance to look at situations that you would never chose to face without getting your hands dirty. Here's your chance to experience things vicariously that would cost you body, soul or life to experience and maybe... avoid, identify with or recover from or perhaps have empathy for people who have actually been there.
An author is NOT his work. At his best an author is a catalyst to help the reader see and understand with different eyes. At his worst he is a propagandist or a pornographer. It is up to the reader to make this determination for himself. If there is truth in his work and an author has applied his craft with heart, then the work will stand or fall on its own merit. As an author all that I ask is that you think for yourself.