Bit Torrent itself isn't illegal. It's just a medium by which people share files. If the files they share aren't theirs to legally share, then the act of sharing them is illegal... not the medium by which they do the sharing.
Napster was shut down because they actually kept files on their servers. That got them in HUGE trouble.
Other companies like Grokster have gotten in trouble because their servers actively enable people to find those files. It "encourages illegal activity".
Bit Torrent... the trackers could get shut down if they move illegal activity, but how can you "shut down" a program that people run that has no servers? You can't.