I may have mentioned this before, but I am a big fan of protagonists with dubious character traits. There is something about a blurry line that adds flavour to their character depth. In fact, if the protagonist was to stop and consider themselves, they would be firmly on the wrong side of that invisible virtuous line.
So in short—I like my protagonist confused.
So here is an interesting analogy to help in the confused protagonist debate: If you are the kind of person who goes to the gym 5 days a week, then going 5 days a week is no big thing. BUT, if you struggle to go once a week, then 5 days in a row is a pretty impressive feat. And so with our protagonist. The more reluctant they are, the more doing something good or heroic chafes, the more interesting it is when they are finally forced to comply.
As a reader, the more confused you are about the protagonist, the more the tension grows. Will they do the right thing? Are they capable of doing the right thing even?
And what about our antagonist? Are they wholly bad? Do they have redeeming qualities? Do you empathise with them at any point in the book? Perhaps their behaviour has been abhorrent, and then you discover a terrible secret about their past that casts new questions onto everything they have so far done.
There is a certain fascination with a good guy, who is far removed from being good. And likewise with a bad guy who is not completely bad.