I see no convincing reason to identify the Roman Catholic Church with the mother of harlots in Revelation 17, certainly not as we know it today. In my judgment, Revelation 17 is about the development of a universal, world church—called a prostitute—that will be opposed to the government of the Beast. Verse 16 says that the Beast (who represents government) will hate the woman and will bring her to ruin and make her naked and desolate, and will eat her flesh and burn her with fire. The “mother of prostitutes,” i.e. the world-church, will be short-lived and ultimately destroyed.
In all likelihood, elements of apostate Protestantism and the Roman Catholic Church and perhaps other religious traditions will comprise the future religious organization designated as the mother of prostitutes.