ISAs spring to mind. That's a deliberate case where something would normally be taxed, but there's an exemption.
Another is corporation tax where you allow companies to claim against it (for R&D activities, for example, because you want to encourage R&D).
I think it makes perfect sense to tax the activity of vaping less than the act of smoking tobacco, since it looks like vaping is less harmful. I'm not sure whether that reduced tax should be zero or not.
I see tobacco tax as seeing this thing that you really can't practically ban in the short term, so you want to discourage it. It seems logical to discourage it socially (make it less convenient by banning it inside pubs and restaurants and so on) and taxing it rather heavily. I agree if it (or alcohol) were a new thing it would likely just not be allowed, but that's not where we are.