Roy is definitely a bad guy in Angels in America: he's selfish, hypocritical, racist, vicious, and manipulative. Though in the end, most audiences probably come to sympathize (at least a little bit) with him on his deathbed, 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. He does give Belize a hard time about the AZT, but his resistance isn't particularly effective. For most of Perestroika, Roy just hangs out in his hospital room arguing with Belize and the ghost of Ethel Rosenberg while he slowly withers away.
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 want to succeed.