Believe me, as a white South African who had nothing to do with apartheid, I know exactly what that feels like.
It is no fun being blamed, shamed and hated for something that you had no hand in.
However, unfortunately, just like there are some who will continue to blame me for a regime that ended before I ever reached high school, there will continue to be people who will see all Muslims as a threat.
Their reasoning is (wrongly or rightly) that while not all Muslims are terrorists, all of the most visible terrorist groups today are self identified Muslims.
I wish I knew what to tell you. How you could make the stigma go away. However, I don't.
Just as I blame the apartheid government and the current racist government for being the catalysts and perpetuators of anti white sentiment in South Africa, you have a dual fight on your hands.
On the one hand, decent, moderate Muslims need to get involved in eradicating the bad apples that are spoiling your particular barrel, and you need to change everyone else's minds.
I don't envy you your task, but try to remember that you can't blame the people who don't know any better. Blame the people who create the stigma and those who perpetuate it, and get involved in the outcry against it. Be vocal in condemning it. If not, don't be surprised if your silence is taken as tacit agreement.