How to clean a BMX bike when its rusted?

I have a Haro Mirra 540 and there is small rusting spots on the bike. How can i get the rust off permanently? I sprayed WD-40 on the frame and scrubbed it with an SOS pad and it still didnt clean all the rust.... It just took the paint off the frame! What can I do to keep this nice bike looking like a nice bike?
 
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