imo, trying to determine a 'good guy' faction in VTM is futile and flawed at its core. None of the sects can be 'good guys' because everyone is a literal bloodsucking monster by default.
There are individuals (including inside of the sects) that may follow a path of humanity, and even then, they are 'human' in comparison to the others among their kind. Mortal notions of morality and 'goodness' don't always function outside of a stable status quo even amongst the mortals, let alone for vampires navigating their own world with its own unique history and politics among the clans and the sects.
The Camarilla and The Sabbat are usually, obviously, accepted as 'bad' but the Anarchs are not 'good'. They were once the same as the Sabbat and while now they usually lack the cult aspect and generally accept that they have to conceal their nature, they can still be very violent and have schemes of their own. They simply don't want to follow the laws of the Camarilla because they don't wish to be constrained. They object to the Camarilla's lack of personal freedom, not their lack of morality.
A lot of disdain for the Camarilla comes from their desire to wear a mask of civility over their monstrous nature and actions, as well as their more rigid laws and hierarchy. Most vampires that choose to be with any of the sects, want to be on the top of the chain or seek security and resources that an individual path does not provide, they simply have to decide how they want to do it depending on which set of principals appeals to them the most.
