ISPs (I work for one) dislike traffic, which heavily saturate channels. Total uplink capacity is comparable with total customer demand at peak hours. So, ISPs have to distinct between immediate (VoIP, gaming, SSH), normal priority (web browsing, email) and bulk (BitTorrent et al) cases. Although, throttling to pre-defined per-customer value seem like stupid idea, but putting them into different buckets is a must.

ISPs also dislike high-PPS low-packet-size (significantly lower than MTU) UDP traffic of uTorrent's uTP protocol, because it quite negatively affects the network hardware.

And, most important — ISPs, in fact, love P2P traffic when it happens between their peers, because such traffic does not consume uplink channels. When it's legally possible — they endorse it (for example, by setting up gaming servers or introducing locally-hosted software-update mirrors), when it's a gray waters of file sharing — they just don't stick their nose in other's business (unless law enforcement requests them so). Of course that's unless they want to make customers dissatisfied their service as network connectivity providers.