Roy is definitely the bad guy in Angels in America; he's selfish, hypocritical, racist, vicious, and manipulative. Although most audiences come to sympathize with him as he becomes sicker and sicker, he's not the first guy you'd invite over for a barbecue. We have to point out, however, that none of this necessarily makes him the play's antagonist. Just because he's a jerk doesn't mean he fits this dramaturgical role.
Roy is not an antagonist in the traditional sense because he's not working against a protagonist in any way. In Millennium Approaches, his central action is to try to get Joe to take a job in the Justice Department in Washington, DC. Sure, it's for Roy's own nefarious purposes, but he's not directly stopping a protagonist from getting what he or she wants, like a traditional antagonist would.
In a way, Roy seems to work as an antagonist on a larger level: he represents the kind of corrupt brand of conservatism that this progressively-minded play is out to debunk. The play treats his character relatively fairly – it's not like he's totally unlikable – but we're not asked to root for him in any way. The characters on the other side of the political spectrum, although flawed, definitely seem to be the ones that the play wants us to root for.