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ShardPhoenix comments on Case study: Folding@home - Less Wrong
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It costs up to a billion dollars (http://en.wikipedia.org/wiki/Drug_development) and up to 14 years (http://www.addictiontreatmentmagazine.com/addiction-treatment/what-it-takes-to-bring-new-treatment-drugs-to-market/) to create a new drug once the basic idea is discovered, and seeing as the companies doing this stay in business, that level of investment must be (reasonably) worthwhile economically. Folding is a drop in the bucket compared to that and even if it never achieves anything serious and is eventually shut down, it seems like it was worth trying - and there's still a chance that it could discover something important about proteins.
edit: Also at best you don't seem to have any better justification for thinking that the probability of significant success is astronomically low than I do for thinking that it's low but not astronomically so, so this aspect of the argument isn't really going anywhere.
Folding has already incurred somewhere around $100m in total expenses. Do the Bayesian update on a 1/10th chance not happening... It's not epsilon or zero, I'll tell you that!
Let me ask you something. I know what evidence would convince me that Folding was a good idea: show me a drug based on Folding results or a therapy change or something like that. But is there any evidence that could convince you that Folding is not a good idea? Because everything you've said seems like it could apply to any project.