According to the NIS, when Amsterdam's smoking ban goes into effect in July, only tobacco will be targeted. Spliff-smokers – much more common in Europe than in the US, as it's only way to smoke hashish without a pipe – must light up outside, whereas smokers of pure marijuana joints can puff away in peace. Though allowing marijuana but not tobacco might seem bizarre, it's actually more consistent with the relative harm of marijuana and tobacco. Then again, I don't see the Dutch legalizing acid, mushrooms, or ecstasy, despite the fact that they also rank lower on the harm scale.
For more on the Netherlands' schizophrenic drug laws (fun fact: selling marijuana is illegal in the Netherlands!), here's the very comprehensive Wikipedia article.