It's really all in the point of view, I think. THEY truly believe they are the good guys and even now, at the end of season four, we can't be 100% sure about who is good and who is bad. When we first met Ben, I emphatically believed there was nothing they could do to redeem the character. But they are, to a degree, slowly chipping away at that and at least leaving the possibility open. A lot of that is also due to the talent of Michael Emerson.
There is so much in this show that demands more than one viewing, which is why I buy the DVD set every season. I've been through all of them several times and still learn new things with each viewing.