In this short video, Dr. Peter Boghossian (author of A Manual for Creating Atheists) talks about Micro vs. Macro interventions. Richard Dawkins, Sam Harris, Ricky Gervais... they fire enormous broadsides at religion. Those are fun, enlightening, and only effective as mass communication at the Macro level. If you try these kinds of things with your religious friend over a cup of coffee, you'll hit a brick wall of defensiveness. When Sam Harris stands on a stage in the frame of a YouTube video, he has much less ability to make a person feel threatened than you do over that cup of coffee.
But everyone has a method of drawing conclusions, and everyone wants their method to be sound. Nobody wants to be seen --least of all by themselves -- to be drawing truth from shaky sources or reasoning.
You can help people grow healthy doubts by helping them get better at reasoning and at evaluating sources of fact. You already know how to do this. And the endeavour becomes cooperative, not adversarial.