I've wondered that for a long time. They did start out as a duo. The Buckingham/Nicks album is pretty good. It sounds pretty much like what you'd expect; early songs by Lindsey and Stevie. They joined Fleetwood Mac together. Lindsey was offerred the guitarist position but he insisted that Stevie join as well, and the rest is history.
Since then, I've seen/read/heard many stories about all the relationship troubles within the band, but not a lot of specifics. Apparently Stevie and Mick had a thing, while they were all still in the band together, so maybe that was the start of things. Infidelity sucks, and definitely has broken up its share of couples. But if you're in a band together, the question isn't just whether or not you stay with the person, it's whether you put the band before your personal relationship with this other band member. Clearly both have put the good of the band over their personal issues sometimes, and sometimes not. Lindsey left for a while. I don't know if Stevie ever officially left, but the Buckingham/McVie album has Mick and John on bass and drums; it's basically a Fleetwood Mac album without Stevie.
I saw an interview one time with Lindsey and he was talking about this time when he and Stevie weren't speaking, but the band was working on a new album. Stevie had a song she was working on, but was stuck. It needed something. She went to Lindsey, because she knew he'd come up with something. Lindsey didn't want to help her because he was pissed at her, but he couldn't help himself. He knew exactly what the song needed. So for the band, they both put the personal shit aside and wrote the song together.
Maybe they hate each other because they were twentysomething and would've broken up like any normal couple, but were "forced" to work together all these years, and the resentment kept building and building. Lindsey says a part of him will always love Stevie, and Stevie has expressed a similar sentiment. But right now, the part that hates him is winning.