The bottom line is that there's no such thing as "safe" when it comes to downloading things for free on the Internet. Why? Plain and simple, if you're doing something illegal, there's always a certain amount of risk involved.
Torrents are a specific file format, and don't have anything to do with the "BitTorrent" website or program. In fact, I'd strongly urge you to use an alternative torrent downloading program, like uTorrent. Utorrent is JUST a program for downloading torrents, and it doesn't try to get you to pay under false pretenses for anything, unlike the BitTorrent site.
Torrent files are a different sort of beast from the single files people download on Limewire or Kazaa, but that doesn't make them any less potentially dangerous. With a program like Limewire or Frostwire, you're downloading a single file. The biggest risk is trying to get a video or music file (WMA, in particular) that, when launched, tells you it needs to connect to a URL to download a codec. That's almost always a sure sign that you've got yourself a bogus download - but you're not in any SERIOUS danger if you remember to tell Windows Media Player NOT to download the third-party codec. Downloading programs (EXE files) or archives (ZIP, RAR, ACE) is also a big risk, because these are more commonly the bearers of trojan payloads.
In contrast, a single torrent download can contain HUNDREDS of other files, any number of which can be infected with a trojan or other malware. To the unaware user, that's an even bigger risk than downloading a bogus video or song from a peer-to-peer service like Limewire.
Additionally, torrent file information is shared by trackers. When you click a link to a torrent and begin downloading (and subsequently uploading) files, your ISP, as well as companies like MediaDefender, can very easily monitor what you're sharing. There are also hundreds or even thousands of torrents out there that are "planted" specifically to track who is downloading them - don't be surprised to get a letter from your ISP if you try downloading an Adobe, Microsoft, or Apple product via torrent.
The keys to staying safe when downloading are 1) downloading LEGAL content, be it games, software, or music and 2) downloading from reputable sites. If you're using ANY peer-to-peer service to get commercial movies, music, games, or software, then you're at risk. Use a site like eMusic or iTunes to buy music, buy games from an online service like Steam, and use sites like OSalt.com and Freeware Genius to find FREE alternatives to the programs you'd otherwise try to download with peer-to-peer apps.
Karma can be a real pain in the butt on the 'net, so play it safe and keep your downloads legal.