For starters, rubber toys aren't exactly "safe". They're incredibly porous, can't be 100% sterilized and expire after ~3-4 months with perfect use. If they start to smell, look or taste differently, they're expired and should be thrown away asap.
For new rubber toys that aren't expired, you can wash them with anti-bacterial soap to help fight the smell and cooties. Be sure to also let them air dry on a clean, dry surface that's cool (melted toys are fun, yo).
Personally I've always found rubber toys to have a smell that you can't really ever get rid of. Cyberskin and other 'realistic' materials seem to be the same way. Silicone doesn't have a perceptible smell or taste, isn't porous (medical grade ftw!) and lasts a lifetime with proper care. :thumbleft: I used to review sex toys.