A company, BitTorrent, created a piece of software, BitTorrent, which used the protocol, BitTorrent, for P2P filesharing.
The BitTorrent company at least was created by the guy who created the BitTorrent protocol. I think their early "BitTorrent" software was not, however, the original implementation of that protocol. (Don't quote me on those facts, I'm going off of memory here.)
Later, BitTorrent the company bought/licensed the uTorrent software and distributed it under the name "BitTorrent". (They mercifully incremented the major version number and stopped distributing their earlier software.)
It's not the best naming system.