Gonna make this short and simple.
If you're using a processor that uses more than 4 cores, then your game is going to crash during the first loading screen after you select new game.

To prevent this, type msconfig into the Windows search bar and your system configuration will pop up. Go to Boot, Advanced Options, check the box for Number of Processors, select 4, hit okay, apply, then restart your system.

Once you've restarted, launch the game like normal, start a new game, and you're golden.

Enjoy!

UPDATE:

There has been an update on how to play Prototype 1 on modern hardware.
Here is the link to mod on Nexus: https://www.nexusmods.com/prototype/mods/52?tab=description

If for some reason the link doesn't work in this post, there is another down in the comments from FlickaTyrone.