While Markdavis's numbers are extremely unlikely to be correct, I know that 96.8% legal use of bittorrent protocol is definitely incorrect. Just to make a note, illegal doesn't mean immoral. Actually, I have no problems illegally downloading information off the web, but that is based on my own morals and not what is legal or illegal.
That being said, I think the number of illegal downloads is around 95%, not quite as bad as 99.5%, but still pretty high. It could be lower, but the problem is that it is hard to track without specifically looking at the packets going in and out of a large number of computers and determining whether each packet is legal or illegal, but doing this would remove network neutrality provisions for the isp that did it and open them to being sued by users and copyright owners, some of which might even be both.
I maintain a torrent server to trade my personal files and photos with friends, family and various business files, but most of my information is just downloaded from either my server or from some website or file server. I like having the torrent server, but frankly not enough people are interested in my files to make it of much use. I do see bittorrent used by several companies to distribute patches and the like and there is definitely a legitimate use for the protocol. That being said, it's the manner in which it is used, not the tool itself that makes it legal/illegal. Using a hammer to hammer in a nail, fine, using a hammer to break into a car and steal stuff, not such a good idea. If you get caught illegally downloading material, it's your choice and you will have to bare the consequences. I'm more than happy to have my day in court if I'm caught.