plumsouce, you're hitting it closer to target than you might know.
99% of P2P traffic is copyright violating material. There's no defense for breaking the law. And this gives all of the P2P traffic a really bad name.
The remaining part is a real annoyance: these companies sell a service or a product but deliberately chose not to pay for the distribution or the traffic it generates and instead borrow (some might argue: steal) that capacity from their users. Now those users often are unwittingly duped into this, or chosen due to them having much bandwidth available to them. Few do this as an intentional choice.
How those users are paying for their bandwidth is left out of the equation. If they have a fixed price deal and unlimited usage, they typically don't care and let the ISP run up the extra costs without getting any extra benefit form it.
Those without that flat fee unlimited use will easily get annoyed by it, jst like most companies trying to using their resources for business purposes instead of due to somebody unintentionally starting to supply something to the rest of the world for "free".
What are examples I've run into from non-copyright violating uses of P2P ... skype: Get promoted to supernode and you'll know what I'm talking about.
World of Warcraft: distributes their updates for the game using a P2P network they build from all gamers currently downloading the update with threats to the users to let the P2P happen or face even slower downloads.
There probably are more out there. And I think it's not in the best interest of all of us to allow companies to abuse this and not pay at all for connectivity for their quite profitable services. The difference between these companies and e.g. Google are gigantic. Google and the like pay serious amounts to be connected to the Internet with huge bandwidths around the world. asking them to pay once again for traffic to end-users is like asking them to pay twice for the same service. The examples above are companies that didn't pay once (ok, just for seeding it). Asking them to pay at least once isn't too much to ask IMHO.
Worse if ISPs are made powerless to stop things like P2P traffic it can only mean we all pay the price in the long run. Just imagine Googling for something means you accept to be part of their P2P crawler for the next hour, or using bing means you're a distribution point for the next black Tuesday updates Microsoft needs to distribute, ...
Since the ISP can't act against this anymore they'll have little choice but to slow it all down and/or charge you more.