Great question! The setting acts as one of the many tools in an author's tool box. They can use the wheres and whens of a story to make it more or less accessible to their audience. It can be used as a tool to transport to an entirely different environment or time period.
If the author gives us a dark, difficult setting (think Rochester's home in Jane Eyre) we have an environment ripe for brooding, conflict, and soul searching. If the author gives us a modern day high school, we have an environment we're familar with. The issues presented could be things we encounter in our own lives and find easily accessible.
Make notes as you read. Record not only the concrete wheres and whens, but also your initial reaction to them. Do they scare you? Intrigue? Disgust? Excite? See if these feelings are similar to the book's protaganist's feelings.
Good luck and happy reading!