They're just different antibiotics that work better on slightly different bacteria so it's not that one is preferable to the other - it depends on what it is being used for. Baytril is the only (or one of the only) systemic antibiotics licensed for use in rabbits, septrin is also commonly used though. It sounds as if your vet has just made a judgement call that septrin is more likely to be effective in this instance. Septrin is also easier to give to bunnies as it's banana flavoured!