As a quick band aid to your problem, I have two thoughts:
1. If you have your User's Manual available, read page 38. If not, in Auto Mode, press the i button once or twice depending upon where you are. Place the cursor in the information display and toggle over to and highlight the flash mode icon. Press ok and then select your preferred mode and hit ok again. You may have had the flash off.
2. In auto mode the flash only works when the camera calls for the additional light. So, it's possible that the scene isn't dark enough to call for flash.
Good luck and hopefully someone with more experience with "Auto Mode" and flash can confirm or supplement these recommendations.