There are a number of responsibilities that a writer has. One of these is to understand that whatever you do to make a bad guy unlikable, somebody, somewhere is going to prefer the bad guy to the good guy. And it is the author's responsibility to make allowances for this.
I'm in the process of finishing off my first novel and I would be naive to believe that if people read it, some readers are not going to prefer the antagonists to the protagonists. This is just human nature and an aspect of reading and listening to stories. Who hasn't watched a film and rooted for the bad guy a few times (especially if the story is clumsy, full of cliches and lacking in skill)?
I've been thinking about this recently because I've just got back from a threshing festival. Many people are familiar with the saying: 'sort the wheat from the chaff'. It's a popular saying which originates from Bible times. John the Baptist described Christ in this way...
"His winnowing fork is in his hand to clear his threshing floor and to gather the wheat into his barn, but he will burn up the chaff with unquenchable fire."
I approach all this biblical stuff with the eyes of a writer and perhaps that is a mistake. But the 'wheat'/'chaff' symbolism is mirrored in many stories. Modern literature often attempts to give the protagonists flaws so that the distinction is less obvious. Of course there are anti-heroes too. But skilled writers can create characters who are likable despite having negative characteristics. And in the end, many fictional characters can be reduced to being either wheat or chaff.
Readers are not stupid (maybe some are but I don't want to go into that). On the whole readers know when an author wants them to like a certain character and sometimes (and for eclectic reasons), they will not do what an author wants them to do.
There are many people who believe that Christ is the greatest storyteller who ever lived. I believe this too. This is not just sycophancy (although it can be). Christ's parables have immense depth and contain symbolism, irony and a whole host of techniques which are way beyond the capabilities of storytellers such as myself. Christ also sorts his characters into the strange archetypes of wheat and chaff. There are parallels in his parables - there are worthy and unworthy servants, wise and foolish virgins, there are shrewd managers and persistent widows and unmerciful judges and unforgiving servants and powerful kings and good Samaritans and branches that remain in the vine and branches that are cut off from the vine and good and bad fish. There is wheat and there is chaff.
For the reader who is behaving while listening to a story, it is an easy choice to make - associate with the good Samaritan, the worthy servant, the wise virgin, the branch that remains resolutely part of the vine. For others there is another choice - associate with the cut off branch or associate with the chaff.
A good storyteller instinctively knows that his or her listeners or readers will do this.
So take the distinction between the wheat and the chaff. In reality the wheat is separated from the chaff as it is collected. The grains of wheat are packed into sacks and they go on to be powdered by a millstone and made into bread or shredded-wheat or whatever (see? I've probably even got that wrong - I haven't learned a thing I tell you!). The chaff falls to the ground, is blown away by the wind or else destroyed. The stalks of the wheat are made into straw and usually used as feed for animals (hold on... what about the stalks?!!).
What I'm trying to say (clumsily) is this: It doesn't matter which character you associate with when it comes to stories or parables. It doesn't matter if you associate with the wheat or if you associate with the chaff. Associating with one or the other does not in itself sort the wheat from the chaff.
And that is because of one fact: A good storyteller should know that this happens all the time.
Think happy thoughts.