It means, "we were able to be together without there being problems", in general. Exactly what it means depends on the context.
If people don't like each other or disagree about something,then you'd say something like, "Despite our differences, we got along fine." I you case, with the "but", this is what it means.
Or it can be positive. "I get along very well with her," meaning we like being together an cooperate well.