I thought they were the good guys? *raises eyebrow*
They are more or less like the Vigilantes of Stendarr and the Silver Hand. Bad people claiming to be good just because they hunt vampires. But they are extremely prejudice, torture people(just check out the dead werewolf bodies in both human and beast form, and torture tools in their lairs and even a http://www.uesp.net/wiki/Skyrim:Physicalities_of_Werewolves on dissecting people!). Not to mention, hypocrites. I.E, "we serve the god of mercy but we have none to spare. Walk in the light or we will forcibly drag you to it".
In the end, it is all a point of view.