Many of the best antagonists have something redeeming about them. Something to make the reader like them even if they're rooting against their cause. Often good guys have something that keeps them from being less than perfect, too.

Consider Gone Girl. Is the husband the good guy? Is he the bad guy? Is the wife the good one? The bad one? My perception of these changed throughout the narrative, and I changed what I rooted for during the course of the events.

Another one who does it very well: George RR Martin. You see these people at cross-purposes in the epic for the throne. Some are good. Some are bad. All men must die. If you choose one character to root for, then you might become disappointed when that character fails.

Don't be afraid to give redeeming qualities to your antagonist and flaws to your protagonist. Don't be afraid to give up good and evil labels in order to make believable characters in realistic situations (whether or not we're in a real world scenario).