The quick and superficial answer is that characterization is hard work. For many writers, it is the entire answer. Characterization is hard work, so they focus on the protagonist and let the rest slide, because they believe that the protagonist is the most important character in the story.

For other writers, there's the issue of discomfort. It's not a pleasant thing to realize that in a criminal's mind, his actions can be rationalized or justified. It's much more comfortable to shrug and assure ourselves that criminals are just bad people, who do bad things. It can be even more disconcerting to realize that if you were in the antagonist's position, you could realistically contemplate, or even do, the things a "bad person" does.

There is also the issue of empathy. Not every writer can write characters who act, think, and believe differently than they do, so figuring out reasonable and justifiable motivations for a character whose actions you abhor is a challenge.

But it's a challenge worth taking on. Antagonists who are evil for the sake of being evil don't lead to plausible conflicts, they lead to comic-book conflicts. This is perfectly acceptable if you're intending to write a superhero comic and "Mua-ha-ha-ha!" is an integral part of your supervillain's vocabulary, but is not usually acceptable in other genres.

(Don't get me wrong: I think superhero comics are great fun, but they're not the style of writing under discussion.)

It's very hard to get the reader to believe in an antagonist when that antagonist is pure, unadulterated evil. Everybody - protagonist, antagonist, sidekick, and all the other characters - have a motivation driving their actions in a story. "Because he's evil" or "because he wants to take over the world" just doesn't cut it.

Fixing this plot error is both easy and hard. Easy, because all you have to do is figure out your antagonist's motivation. Hard, because doing that is a lot of work.

In addition to the usual character profiling questions you can ask yourself, or ask your character in a mock interview, you could also try turning your entire story upside down. Reverse the characters' roles, tell the story from the antagonist's point of view. What does the antagonist want? How is the protagonist blocking him? What does the antagonist try, and how is he thwarted? I'm not advocating writing this reversed story in full, but brainstorming, outlining, and maybe writing out a few key scenes with the antagonist as hero.

Doing this may force you to re-think your plot - but the end result will be stronger for it.