Frank went through an extremely messy divorce from his first wife up to and including alleged domestic abuse.
The common theories for are some variation/combination of:
* He can't do better. He's still a weird manchild and John indulges that part of him while a gold digger may not-he doesn't make that much (~$150k/year) and has surprisingly little savings for someone of his age and income.
* Frank knows about John's incompetence and sordid personal past, and that gives him absolute leverage/control over him. His ex-wife has also described him as controlling in the extreme and alleges he has tried to keep her from getting into the science fiction writing scene.
* Fetish. Some of Frank's comments on John's now deleted LiveJournal give the impression that he enjoyed, if not got off to, the idea of transforming someone to that extent, and his artwork of John is also deeply messed up
There is also a "mutually assured destruction" aspect to a potential divorce: Frank and John know about each other's pasts, so neither could leave without both their reputations getting destroyed.