PETA certainly does piss off a lot of people, but that's their point. Trying to never offend anyone means never getting people's attention.
(In my experience, I've found that people, art, ideas, et al that are truly remarkable always have rabid critics.)
They actually helped convince me to become a vegetarian. I also think their greatest strength is putting pressure on various companies to stop selling fur or testing on animals.
I admire their ad campaigns, too.
The one thing I think they mess up is not being better about picking their battles.
For instance, they criticized Chris Christie for killing a fly. I do think flies are one of God's creatures, and I try to avoid killing them.
But making a "thing" over it was, imo, a huge PR