I believe the latest thinking is that the mucosal layer in your gut is weak, which allows bacteria to infiltrate it, and contact your actual intestines, which then elicits an immune response.
gut.bmj.com/content/early/2013/02/19/gutjnl-2012-303207.fullFlagyl kills that bacteria off, calming the immune response. But, like PathogenKiller said, if you keep up the flagyl, you'll eventually kill off enough commensal bacteria to render your gut defenseless, and then you'll be in a constant flare.
One theory of healing is that an FMT can help restore the bacterial balance and, presumably, the mucosal layer, so that you (ideally) don't have UC anymore.