Virtual Mouse Input Prevention - bypass?

Hey guys. I've played a lot of different MMOs, and have had to deal with many different types of hack prevention, but this one thing has stood out to me among all the games I've played:

My physical mouse has always worked.

Even in games with tons of different ways to stop automation I've never had a problem with my physical mouse not working in game. Can anyone explain:

1. why
2. how can I direct programmatic input in the same manner as my physical mouse in such a way that it always works?

Basically, it seems to me there should be a simple solution to making any automated inputs look as though they originated with a physical mouse or keyboard, why isn't there?

@warbeak1245
Yea its possible but i'v not tried it yet.

Basically a flag is set telling the game the input was injected.
Read this if you haven't already.
UsualSuspect - Pastebin.com

Sorry for grave digging, but just make you're own mouse hook, run it after the game, have it change the input from injected to the default (I forget what that is) and it'll be passed to the next mouse hook (probably the MMO) and it'll see it as a standard click.