We decided that downvoting is often a good idea: Downvoting is good for you (and for the site)!
Does it make sense that people lose reputation when they downvote if we want to encourage them to downvote more frequently?
The -1 cost is so minimal that I am always surprised when this comes up.
Anyway, the point is to downvote only when you feel strongly, not on a whim. I feel the -1 cost of a downvote (plus the higher rep requirement to downvote at all) works quite well in this regard.
As to whether there should be more downvoting, I think that's an education issue within your community.
edit: downvotes on questions now no longer cost rep. See http://blog.stackoverflow.com/2011/06/optimizing-for-pearls-not-sand/
The downvote cost is minimal, and ensures that people only do it when they mean it. This topic has been covered on meta.stackoverflow.com.
Here's a quote from the question you linked to:
But what about the rep loss?
While downvoting costs you a tiny bit of reputation, it is still, by a very large margin, a net gain. Think of how much time you've spent on this website already. Think of how much you've learned since you're on this site. Think of how we're making the Internet a better place. As Phil Plait said, we're making the world more reality-based, post by post.
For me it isn't very clear, when to downvote a question and when to vote to close it.
Well - maybe an interesting question which is badly worded, but fits to kind of questions we encourage, could be downvoted, without voting to close.
In both cases we should try to be objective, and not just downvote to express, that we're not interested in a theme. Not upvoting a fine question for some health-and-diet-theme seems ok for me.
Well, and inappropriate questions should be voted to close. Maybe, if your vote to close is ignored or the majority decides to reopen it, you can downvote a question.