Oh, don't get me wrong, I like a good guy to root for too (even said so previously
). But ambiguity can make a story more interesting, realistic, and complex. And as others have said there can be good characters but ambiguous situations. And sometimes good people have to do nasty things.
The book series I'm currently reading, there seems to be NOBODY really who is a "good guy" to root for. Everybody, even the MC who starts out sympathetic and with good intentions, seems corrupt and opportunistic. I really hope something changes by the end of the series because I find it so bleak. Ambiguity, yes, love it, but I prefer a LITTLE clarity here and there. At the moment, I'm really not liking the protagonist, not even in a "What a horrific jerk! I love him!" kind of way. I'm not finding myself wanting to root for anybody, and that's bothersome.
I think ambiguity is good when it makes the reader think, but when it just makes the reader think, "Why should I like (even in a twisted way) any of these people?" then it might have gone too far.