To me, because everyone is so jumpy about it..it means I'm probably correct....just sayin
afraid? silence the opposition
No, of course not. You just said nobody was going to care if patents were being infringed because they use torrents for copyright infringement. No, you never said the word "all", but you did ask why this would change anything, which would be quite strange if you were at all considering, say, Blizzard.
Of course, this is before we even start to get in on your apparent conflation of the end users (who would be the ones committing copyright infringement with the software) and the developers (who would be the ones allegedly committing patent infringement).
And, because it's really not worth starting another comment for it: your automatic assumption that downvotes == people trying to silence the opposition and your subsequent goading are really childish. HN is, for the most part, a sane, sensical, and mature community and it reflects poorly on everyone when you make such baseless assumptions. Have you considered reflecting on what your comment adds or detracts from the conversation? I think you'll find that it adds little while the "everyone is so jumpy about it means I'm right" comment is an inane way to curb conversation.
One of the greatest mistakes one can make, in my opinion, is believing that opposition equals justification. It's the "I know I'm right because they all think I'm wrong" argument that is a favorite of nutjobs everywhere. Don't get me wrong, there are times when a small minority is more right than a large majority, but this is not one of those times.
Now things like FTP, google, and the web are also used for piracy, but I'm not going to say that the majority of sites out there are for pirated materials.
Do these outnumber the pirates? I don't really have the figures to even start commenting on that. But I think it's pretty clear that it'll make some difference if the BitTorrent protocol is found to be infringing on some patents.