"If you're running from a cop, you must be guilty. Right?" - Guilty or not is for judge and jury to decide. So far the only charge will be "fleeing/evading the police".

"Which means you're a criminal" - you are not a criminal unless convicted.

"which means you're probably a serious threat to others." - 'probably' is the key word. Cops cannot shoot people because they are probably dangerous. "Probable cause to believe" is not the same as "probably".