If your car was stolen, even by a family member, and you have comprehensive and collision coverage on the car, the insurance company should pay for the damages to your car less your deductible.
Since this was a family member, you will need to file a police report for the theft. The police may arrest him or not, but the report still needs to be filed. However, even if not a family member, a police report should be filed if you have not already done so.
If you have previously allowed your son to use the car, there could be an issue with the police and the insurance company. He may have felt he was allowed to use the car and did not consider that he was stealing it. If he lives with you that could make his case stronger against a theft charge. However, your collision coverage should still cover the car if he was a licensed driver.