The Microsoft Flight Simulator 3.1 version is very old therefore modern systems might have issues running it. I recommend downloading the patch through the websites listed on Google. It's said it enhances functionality and compatibility. Additionally, apply a compatibility tweak to the game. Right click the main executable and go to Properties > Compatibility. Choose a prior version of Windows and then try launching the game this way.
I recommend getting the FSX version of Microsoft Flight Simulator. It's an updated version to support modern operating systems with enhanced graphics and features.