If you wish to join PunkBuster ON servers, then you have to run PunkBuster, otherwise it will kick you.
Head to punkbuster.com and click the Download PBSetup button, and select the option “For All Windows Games."
Open pbsetup.zip, then run pbsetup.exe. Accept the EULA, follow the instructions, update PunkBuster, and then click Add a Game.
In the drop down menu, select Battlefield 3, then Add Game, and finally, before trying to run Battlefield 3 again, Check for Updates.
If you wish to join PB OFF servers, then you don't have to do any of these.