I think it might have to do with the fact that, physiologically, salvia is quite harmless. Marijuana, on the other hand, can effect significant changes in the brain. Keeping in mind that salvia hasn't really undergone anywhere near the amount of testing that cannabis has, so further study might come up with more "damning" evidence against salvia.
Also, what someone said about it not being a recreational drug. It's "interesting", but not a lot of "fun". So it's not as exciting for the government to rush to quash it's use :P But seriously, for that reason there aren't really issues with "abuse" of salvia, which is a key determinant in government banning a substance.
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